101
|
Raya D, Shreya A, Kumar A, Giri SK, Salem DR, Gnimpieba EZ, Gadhamshetty V, Dhiman SS. Molecular regulation of conditioning film formation and quorum quenching in sulfate reducing bacteria. Front Microbiol 2022; 13:1008536. [PMID: 36386676 PMCID: PMC9659907 DOI: 10.3389/fmicb.2022.1008536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/26/2022] [Indexed: 09/19/2023] Open
Abstract
Sensing surface topography, an upsurge of signaling biomolecules, and upholding cellular homeostasis are the rate-limiting spatio-temporal events in microbial attachment and biofilm formation. Initially, a set of highly specialized proteins, viz. conditioning protein, directs the irreversible attachment of the microbes. Later signaling molecules, viz. autoinducer, take over the cellular communication phenomenon, resulting in a mature microbial biofilm. The mandatory release of conditioning proteins and autoinducers corroborated the existence of two independent mechanisms operating sequentially for biofilm development. However, both these mechanisms are significantly affected by the availability of the cofactor, e.g., Copper (Cu). Generally, the Cu concentration beyond threshold levels is detrimental to the anaerobes except for a few species of sulfate-reducing bacteria (SRB). Remarkably SRB has developed intricate ways to resist and thrive in the presence of Cu by activating numerous genes responsible for modifying the presence of more toxic Cu(I) to Cu(II) within the periplasm, followed by their export through the outer membrane. Therefore, the determinants of Cu toxicity, sequestration, and transportation are reconnoitered for their contribution towards microbial adaptations and biofilm formation. The mechanistic details revealing Cu as a quorum quencher (QQ) are provided in addition to the three pathways involved in the dissolution of cellular communications. This review articulates the Machine Learning based data curing and data processing for designing novel anti-biofilm peptides and for an in-depth understanding of QQ mechanisms. A pioneering data set has been mined and presented on the functional properties of the QQ homolog in Oleidesulfovibrio alaskensis G20 and residues regulating the multicopper oxidase properties in SRB.
Collapse
Affiliation(s)
- Dheeraj Raya
- Department of Civil and Environmental Engineering, South Dakota Mines, Rapid City, SD, United States
- 2DBEST Research Center, South Dakota Mines, Rapid City, SD, United States
| | - Aritree Shreya
- Department of Civil and Environmental Engineering, South Dakota Mines, Rapid City, SD, United States
- 2DBEST Research Center, South Dakota Mines, Rapid City, SD, United States
| | - Anil Kumar
- Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Shiv Kumar Giri
- Department of Biotechnology, Maharaja Agrasen University, Baddi, Himachal Pradesh, India
| | - David R. Salem
- Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD, United States
| | - Etienne Z. Gnimpieba
- 2DBEST Research Center, South Dakota Mines, Rapid City, SD, United States
- Department of Biomedical Engineering, University of South Dakota, Vermillion, SD, United States
| | - Venkataramana Gadhamshetty
- Department of Civil and Environmental Engineering, South Dakota Mines, Rapid City, SD, United States
- 2DBEST Research Center, South Dakota Mines, Rapid City, SD, United States
| | - Saurabh Sudha Dhiman
- Department of Civil and Environmental Engineering, South Dakota Mines, Rapid City, SD, United States
- 2DBEST Research Center, South Dakota Mines, Rapid City, SD, United States
- Department of Chemistry, Biology and Health Sciences, South Dakota Mines, Rapid City, SD, United States
| |
Collapse
|
102
|
Ma Y, Du J, Yin Z, Dai H, Wei Y, Xia Y, Li L, Ye Z, Huang Z. Metallothionein-1 is Positively Correlated with Inflammation and Ankylosing Spondylitis Activity. J Inflamm Res 2022; 15:5935-5944. [PMID: 36274830 PMCID: PMC9585266 DOI: 10.2147/jir.s382827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
Introduction Ankylosing spondylitis (AS) is a common form of chronic inflammatory rheumatic disease. Metallothionein-1 (MT-1) has been known to play an immunosuppressive role in various noninfectious inflammatory diseases, especially osteoarthritis and rheumatoid arthritis, thus inhibiting inflammation and pathogenesis in various diseases. However, whether MT-1 is related to AS is unclear. Here, we examined the levels of MT-1 in patients with AS and its correlation with the disease activity, complication, clinical indexes, and inflammatory cytokines and attempted to explain the effect of MT-1 on inflammation in AS. Methods The messenger RNA (mRNA) and protein expression of MT-1 in patients with AS were detected through real-time polymerase chain reaction and enzyme-linked immunosorbent assay. The associations between serum MT-1 protein level and clinical indexes or proinflammatory cytokines in AS were analyzed using the Spearman correlation test. Results The mRNAs and serum protein levels of MT-1 were significantly higher in patients with AS, especially in patients with active AS and patients with osteoporosis (OP) than in healthy controls (HCs), and no difference was observed between patients with inactive AS and HCs. Serum MT-1 levels positively correlated with disease activity, proinflammatory cytokines, and clinical indexes Ankylosing Spondylitis Disease Activity Score with C-Reactive Protein, C-reactive protein level, and erythrocyte sedimentation rate in patients with AS. Conclusion MT-1 expression was upregulated in patients with active AS but not in those with inactive AS and positively correlated with clinical indexes, especially in OP, as well as with proinflammatory cytokines tumor necrosis factor–alpha, interleukin (IL)-1β, and IL-6 in patients with AS.
Collapse
Affiliation(s)
- Yanmei Ma
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, People’s Republic of China,Biological Therapy Institute, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, Health Science Center, Shenzhen University, Shenzhen, 518055, People’s Republic of China,Joint Research Laboratory for Rheumatology of Shenzhen University Health Science Center and Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518055, People’s Republic of China
| | - Jing Du
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Zhihua Yin
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, People’s Republic of China,Joint Research Laboratory for Rheumatology of Shenzhen University Health Science Center and Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518055, People’s Republic of China
| | - Hanying Dai
- Biological Therapy Institute, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, Health Science Center, Shenzhen University, Shenzhen, 518055, People’s Republic of China
| | - Yazhi Wei
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, People’s Republic of China,Joint Research Laboratory for Rheumatology of Shenzhen University Health Science Center and Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518055, People’s Republic of China
| | - Yuhao Xia
- Biological Therapy Institute, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, Health Science Center, Shenzhen University, Shenzhen, 518055, People’s Republic of China,Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Lingyun Li
- Biological Therapy Institute, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, Health Science Center, Shenzhen University, Shenzhen, 518055, People’s Republic of China
| | - Zhizhong Ye
- Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, People’s Republic of China,Joint Research Laboratory for Rheumatology of Shenzhen University Health Science Center and Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518055, People’s Republic of China,Correspondence: Zhizhong Ye, Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518040, People’s Republic of China, Email
| | - Zhong Huang
- Biological Therapy Institute, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, Health Science Center, Shenzhen University, Shenzhen, 518055, People’s Republic of China,Joint Research Laboratory for Rheumatology of Shenzhen University Health Science Center and Shenzhen Futian Hospital for Rheumatic Diseases, Shenzhen, 518055, People’s Republic of China,Zhong Huang, Department of Immunology, Biological Therapy Institute of Shenzhen University, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Shenzhen University Health Science Center, Shenzhen, 518055, People’s Republic of China, Tel +86-755-86671943, Email
| |
Collapse
|
103
|
Liu C, Liu L. Hypoxia-related tumor environment correlated with immune infiltration and therapeutic sensitivity in diffuse large B-cell lymphoma. Front Genet 2022; 13:1037716. [PMID: 36313435 PMCID: PMC9614142 DOI: 10.3389/fgene.2022.1037716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 09/23/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Due to the high heterogeneity of diffuse large B-cell lymphoma (DLBCL), traditional chemotherapy treatment ultimately failed in one-third of the patients. Big challenges existed in finding how to accurately predict prognosis and provide individualized treatment. Hypoxia, although being a key factor in the development and progression of DLBCL, plays its role in DLBCL prognosis, which has yet to be fully explored. Methods: Data used in the current study were sourced from the Gene Expression Omnibus (GEO) database. DLBCL patients were divided according to different hypoxia-related subtypes based on the expressions of hypoxia-related genes (HRGs) relevant to survival. Differentially expressed genes (DEGs) between subtypes were identified using the limma package. Using univariate Cox regression and least absolute shrinkage and selection operator (LASSO) analyses, the prognostic signature was established to calculate risk scores. The tumor microenvironment (TME) in low- and high-risk groups was evaluated by single-sample gene set enrichment analysis (ssGSEA) and ESTIMATE. The chemotherapeutic sensitivity in two groups was assessed by IC50 values. Results: DLBCL patients were clustered into two hypoxia-related subtype groups according to different gene survival and expressions associated with increasing oxygen delivery and reducing oxygen consumption, and these two subtype groups were compared. Based on the differential expression, a risk model was established using univariate cox and LASSO regression analyses, FNDC1, ANTXR1, RARRES2, S100A9, and MT1M. The performance of the risk signature in predicting the prognosis of DLBCL patients was validated in the internal and external datasets, as evidenced by receiver operating characteristic (ROC) curves. In addition, we observed significant differences in the tumor microenvironment and chemotherapeutic response between low- and high-risk groups. Conclusion: Our study developed novel hypoxia-related subtypes in DLBCL and identified five prognostic signatures for DLBCL patients. These findings may enrich our understanding of the role of hypoxia in DLBCL and help improve the treatment of DLBCL patients.
Collapse
|
104
|
Upregulation of Metallothionein 1 G (MT1G) Negatively Regulates Ferroptosis in Clear Cell Renal Cell Carcinoma by Reducing Glutathione Consumption. JOURNAL OF ONCOLOGY 2022; 2022:4000617. [PMID: 36204178 PMCID: PMC9532108 DOI: 10.1155/2022/4000617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/01/2022] [Accepted: 08/04/2022] [Indexed: 11/18/2022]
Abstract
Ferroptosis is characterized by lipid peroxidation and iron accumulation, closely associated with clear cell renal cell carcinoma (ccRCC). It is of great significance for prognostic prediction and treatment of ccRCC to find biomarkers related to ferroptosis. We conducted several bioinformatic analyses using the transcriptome data and clinical information derived from online databases. Firstly, we identified the differentially expressed target genes in ccRCC. Then, t test and COX analysis were used to determine whether it was an independent prognostic factor combined with clinical information. String and gene set enrichment analysis (GSEA) were used to predict its function. Finally, we used ccRCC cells: 769-P and KAKI-1 in vitro to verify the regulation of target genes on cell proliferation apoptosis, iron metabolism, and GSH metabolism, which were used to judge the effect of target genes on ferroptosis. The study showed that MT1G is downregulated in ccRCC tissues compared with normal renal tissues. However, the ccRCC patients with higher expression relatively had higher malignancy and advanced stages. MT1G is an independent adverse factor for the prognosis of ccRCC. The protein interaction network analysis and GSEA showed that MT1G was closely related to GSH metabolism-related proteins (GSR) and lipid oxidation-related proteins (PLA2G2A). Samples with high expression of MT1G were enriched in “glutathione metabolism,” “oxidative phosphorylation,” and “proteasome,” whose function was involved in GSH metabolism and lipid peroxidation. The term associated with the occurrence and development of tumors included “P53 signaling pathway.” Furthermore, in vitro experiments showed that MT1G partially blocked ferroptosis induced by erastin and sorafenib-induced ccRCC cell lines (769-P and CAKI-1). The mechanism may be that MT1G affects ferroptosis by regulating GSH consumption in ccRCC cells. MT1G may be a negative regulator of ferroptosis in ccRCC cells and a biomarker of poor prognosis.
Collapse
|
105
|
Zhang S, Xu X, Li Z, Yi T, Ma J, Zhang Y, Li Y. Analysis and Validation of Differentially Expressed Ferroptosis-Related Genes in Regorafenib-Induced Cardiotoxicity. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:2513263. [PMID: 36204517 PMCID: PMC9530921 DOI: 10.1155/2022/2513263] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/29/2022] [Indexed: 11/18/2022]
Abstract
Background Although tyrosine kinase inhibitors (TKIs) constitute a type of anticancer drugs, the underlying mechanisms of TKI-associated cardiotoxicity remain largely unknown. Ferroptosis is a regulated cell death form that implicated in several tumors' biological processes. Our objective was to probe into the differential expression of ferroptosis-related genes in regorafenib-induced cardiotoxicity through multiple bioinformatics analysis and validation. Methods and Materials Four adult human cardiomyocyte cell lines treated with regorafenib were profiled using Gene Expression Omnibus (GEO) (GSE146096). Differentially expressed genes (DEGs) were identified using DESeq2 in R (V.3.6.3). Then, Gene Ontology (GO) Enrichment Analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) Enrichment Analysis, and Gene Set Enrichment Analysis (GSEA) were used to explore DEGs' bioinformatics functions and enriched pathways. We intersected DEGs with 259 ferroptosis-related genes from the FerrDb database. Finally, the mRNA levels of differentially expressed ferroptosis-related genes (DEFRGs) were validated in regorafenib-cultured cardiomyocytes to anticipate the link between DEFRGs and cardiotoxicity. Results 747,1127,773 and 969 DEGs were screened out in adult human cardiomyocyte lines A, B, D, and E, respectively. The mechanism by which REG promotes cardiotoxicity associated with ferroptosis may be regulated by PI3K-Akt, TGF-beta, and MAPK. GSEA demonstrated that REG can promote cardiotoxicity by suppressing genes and pathways encoding extracellular matrix and related proteins, oxidative phosphorylation, or ATF-2 transcription factor network. After overlapping DEGs with ferroptosis-related genes, we got seven DEFRGs and found that ATF3, MT1G, and PLIN2 were upregulated and DDIT4 was downregulated. The ROC curve demonstrated that these genes predict regorafenib-induced cardiotoxicity well. Conclusion We identified four DEFRGs which may become potential predictors and participate in the regorafenib-induced cardiotoxicity. Our findings provide possibility that targeting these ferroptosis-related genes may be an alternative for clinical prevention and therapy of regorafenib-related cardiotoxicity.
Collapse
Affiliation(s)
- Siyuan Zhang
- The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150000, China
| | - Xueming Xu
- The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150000, China
| | - Zhangyi Li
- Department of Biochemistry and Life Sciences, Faculty of Arts and Sciences, Queen's University, Kingston, Ontario, Canada 91761
| | - Tian Yi
- Harbin Medical University, Harbin, Heilongjiang 150000, China
| | - Jingyu Ma
- The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150000, China
| | - Yan Zhang
- The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150000, China
| | - Yilan Li
- The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150000, China
- Key Laboratory of Myocardial Ischemia, Ministry of Education, Harbin Medical University, Harbin, Heilongjiang 150000, China
| |
Collapse
|
106
|
Cong T, Luo Y, Fu Y, Liu Y, Li Y, Li X. New perspectives on ferroptosis and its role in hepatocellular carcinoma. Chin Med J (Engl) 2022; 135:2157-2166. [PMID: 36525603 PMCID: PMC9771279 DOI: 10.1097/cm9.0000000000002327] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Indexed: 12/23/2022] Open
Abstract
ABSTRACT For a long time, the morbidity and mortality rates of hepatocellular carcinoma (HCC) have remained high. Since the concept of ferroptosis was introduced in 2012, researchers' perspectives have shifted toward finding novel ferroptosis-related treatment strategies, especially for tumors that are resistant to apoptosis. In recent years, there have been an increasing number of studies on ferroptosis, and these studies have found that ferroptosis has great potential and promise for cancer treatment. Ferroptosis is a kind of regulated cell death (RCD); unlike apoptosis, ferroptosis is an iron-dependent type of RCD driven by lipid peroxidation. The whole process of ferroptosis mainly revolves around three pathways (system xc-/ glutathione peroxidase 4 [GPX4]), lipid peroxidation, and iron metabolism), which are also regulated by various metabolic factors. This review will attempt to analyze the relationship between the system xc-/GPX4 pathway, lipid peroxidation, iron metabolism, and ferroptosis from three aspects (triggering, execution, and regulation), and the regulatory factors for ferroptosis will be summarized. In this review, we will also illustrate the relationship between ferroptosis and tumors as well as its application in tumors from the perspective of HCC. Finally, we will summarize the current limitations and needs and provide perspectives related to the focus of development in the future.
Collapse
Affiliation(s)
- Tianhao Cong
- Department of Interventional Therapy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yingen Luo
- Department of Interventional Therapy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yan Fu
- Department of Interventional Therapy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yu Liu
- Department of Interventional Therapy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yujie Li
- Department of Interventional Therapy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xiao Li
- Department of Interventional Therapy, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| |
Collapse
|
107
|
A Novel Prognosis Signature Based on Ferroptosis-Related Gene DNA Methylation Data for Lung Squamous Cell Carcinoma. JOURNAL OF ONCOLOGY 2022; 2022:9103259. [PMID: 36131791 PMCID: PMC9484906 DOI: 10.1155/2022/9103259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/07/2022] [Accepted: 07/13/2022] [Indexed: 11/18/2022]
Abstract
Ferroptosis-related genes regulating an iron- and lipid reactive oxygen species (ROS)-dependent form of programmed cell death suggest critical roles for ferroptosis in cancers. However, the prognostic value of ferroptosis-related epigenetic features such as DNA methylation in lung squamous cell carcinoma (LUSC) needs to be studied. Ferroptosis-related genes are collected from the FerrDb database, and the methylation data of these related genes in LUSC methylation data downloaded from the TCGA are retrieved. The DNA methylation data (362 LUSC samples) were analyzed to screen prognostic ferroptosis-related methylation sites. After patients with complete overall survival (OS) information were randomly separated into training cohort (n = 200) and validation cohort (n = 162), the least absolute shrinkage and selection operator (LASSO) and the Cox regression were used to establish and validate the prognostic signature. The time-dependent receiver operating characteristic (ROC) and Kaplan–Meier survival curve analyses, Harrell's concordance index (C-index), calibration analysis, and decision curve analysis (DCA) were performed to evaluate the risk signature and related nomogram. A series of other bioinformatics approaches such as mexpress, cbioportal, maftools, string, metascape, TIMER, and Kaplan–Meier survival curve analysis were also used to determine the methylation, mutation status, protein interaction network or functional enrichment, effects on immune cell infiltration, or expression level prognosis of those signature-related genes. A total of 137 DNA methylation sites were identified as prognostic predictors corresponding to 109 ferroptosis-related genes (FRGs). The methylation signature containing 31 methylation sites proved to be superior predictive efficiency in predicting the 1-, 3-, 5-, and 10-year OS. 8 out of 28 signature-related genes were significantly related to OS time or OS state in patients with LUSC. In addition, DUSP1, ZFN36, and ALOX5 methylation status also correlated with pathological M and ALOX5 methylation correlated with pathological N. The prognostic prediction efficiency of T, N, M, and the stage was inferior to that of the DNA methylation signature. LUSC patients in the high-risk group own a significantly larger number of variants of FRGs than those in the low-risk group. In addition, negative or positive correlation patterns were presented among the different infiltrating immune cells with risk scores or signature-related genes in patients with LUSC. The expression level of 15 signature-related genes showed a significant relationship with OS of LUSC patients. A novel prognostic nomogram survival model containing 4 factors including age, pathologic T, stage, and risk group was constructed and validated, AndC-index, decision curve analysis (DCA), and calibration analysis demonstrated its excellent predictive performance. The FRG DNA methylation data-based prognostic model acts as a powerful prognostic prediction indicator in LUSC patients and is advantageous over the traditional model based on T, N, M, and stage.
Collapse
|
108
|
Dissecting Molecular Heterogeneity of Circulating Tumor Cells (CTCs) from Metastatic Breast Cancer Patients through Copy Number Aberration (CNA) and Single Nucleotide Variant (SNV) Single Cell Analysis. Cancers (Basel) 2022; 14:cancers14163925. [PMID: 36010918 PMCID: PMC9405921 DOI: 10.3390/cancers14163925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/04/2022] [Accepted: 08/11/2022] [Indexed: 12/27/2022] Open
Abstract
Circulating tumor cells' (CTCs) heterogeneity contributes to counteract their introduction in clinical practice. Through single-cell sequencing we aim at exploring CTC heterogeneity in metastatic breast cancer (MBC) patients. Single CTCs were isolated using DEPArray NxT. After whole genome amplification, libraries were prepared for copy number aberration (CNA) and single nucleotide variant (SNV) analysis and sequenced using Ion GeneStudio S5 and Illumina MiSeq, respectively. CTCs demonstrate distinctive mutational signatures but retain molecular traces of their common origin. CNA profiling identifies frequent aberrations involving critical genes in pathogenesis: gains of 1q (CCND1) and 11q (WNT3A), loss of 22q (CHEK2). The longitudinal single-CTC analysis allows tracking of clonal selection and the emergence of resistance-associated aberrations, such as gain of a region in 12q (CDK4). A group composed of CTCs from different patients sharing common traits emerges. Further analyses identify losses of 15q and enrichment of terms associated with pseudopodium formation as frequent and exclusive events. CTCs from MBC patients are heterogeneous, especially concerning their mutational status. The single-cell analysis allows the identification of aberrations associated with resistance, and is a candidate tool to better address treatment strategy. The translational significance of the group populated by similar CTCs should be elucidated.
Collapse
|
109
|
Maurya VK, Szwarc MM, Fernandez-Valdivia R, Lonard DM, Song Y, Joshi N, Fazleabas AT, Lydon JP. Early growth response 1 transcription factor is essential for the pathogenic properties of human endometriotic epithelial cells. Reproduction 2022; 164:41-54. [PMID: 35679138 PMCID: PMC9339520 DOI: 10.1530/rep-22-0123] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/09/2022] [Indexed: 01/13/2023]
Abstract
Although a non-malignant gynecological disorder, endometriosis displays some pathogenic features of malignancy, such as cell proliferation, migration, invasion and adaptation to hypoxia. Current treatments of endometriosis include pharmacotherapy and/or surgery, which are of limited efficacy and often associated with adverse side effects. Therefore, to develop more effective therapies to treat this disease, a broader understanding of the underlying molecular mechanisms that underpin endometriosis needs to be attained. Using immortalized human endometriotic epithelial and stromal cell lines, we demonstrate that the early growth response 1 (EGR1) transcription factor is essential for cell proliferation, migration and invasion, which represent some of the pathogenic properties of endometriotic cells. Genome-wide transcriptomics identified an EGR1-dependent transcriptome in human endometriotic epithelial cells that potentially encodes a diverse spectrum of proteins that are known to be involved in tissue pathologies. To underscore the utility of this transcriptomic data set, we demonstrate that carbonic anhydrase 9 (CA9), a homeostatic regulator of intracellular pH, is not only a molecular target of EGR1 but is also important for maintaining many of the cellular properties of human endometriotic epithelial cells that are also ascribed to EGR1. Considering therapeutic intervention strategies are actively being developed for EGR1 and CAIX in the treatment of other pathologies, we believe EGR1 and its transcriptome (which includes CA9) will offer not only a new conceptual framework to advance our understanding of endometriosis but will also furnish new molecular vulnerabilities to be leveraged as potential therapeutic options in the future treatment of endometriosis.
Collapse
Affiliation(s)
- Vineet K. Maurya
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Maria M. Szwarc
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | | | - David M. Lonard
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Yong Song
- Department of Obstetrics, Gynecology & Reproductive Biology, Michigan State University, Grand Rapids, Michigan
| | - Niraj Joshi
- Department of Obstetrics, Gynecology & Reproductive Biology, Michigan State University, Grand Rapids, Michigan
| | - Asgerally T. Fazleabas
- Department of Obstetrics, Gynecology & Reproductive Biology, Michigan State University, Grand Rapids, Michigan
| | - John P. Lydon
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA,Correspondence should be addressed to JP Lydon;
| |
Collapse
|
110
|
Zhu J, Liu L, Ma J, Fu Q, Zheng Z, Du E, Xu Y, Zhang Z. Biotransformation of graphene oxide within lung fluids could intensify its synergistic biotoxicity effect with cadmium by inhibiting cellular efflux of cadmium. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119421. [PMID: 35533959 DOI: 10.1016/j.envpol.2022.119421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/23/2022] [Accepted: 05/03/2022] [Indexed: 06/14/2023]
Abstract
Graphene oxide (GO) has been widely studied and applied in numerous industrial fields and biomedical fields for its excellent physical and chemical properties. Along with the production and applications of GO persist increasing, the environmental health and safety risk (EHS) of GO has been widely studied. However, previous studies almost focused on the biotoxicity of pristine GO under a relatively high exposure dose, without considering its transformation process within environmental and biological mediums. Meanwhile, its secondary toxicity or synergistic effects have not been taken seriously. Here, two different kinds of artificial lung fluids were adopted to incubate pristine GO to mimic the biotransformation process of GO in the lung fluids. And, we explored that biotransformation within the artificial lung fluids could significantly change the physicochemical properties of GO and could enhance its biotoxicity. To reveal the synergistic effects of GO and toxic metal ions, we uncovered that GO could enhance the intracellular content of metal ions by inhibiting the efflux function of ATP binding cassette (ABC) transporters which are distributed on the cellular membrane, and artificial lung fluids incubation of GO could enhance this synergistic effect. Finally, toxic metal ions induced a series of toxic reactions through oxidative stress response and promoted cell death. Moreover, consistent with the results of in vitro experiments, the lungs of mice exposed to GOs combined with Cd exhibited significant inflammation and oxidative stress compared with Cd treatment alone, and it was more remarkable within the mice which were treated with bio-transformed GOs. In summary, this study explored the impact and mechanism of biotransformation of GO in the lung fluids on the synergistic and secondary effects between GO and metal ions.
Collapse
Affiliation(s)
- Jianqiang Zhu
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, 300211, China
| | - Leyi Liu
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, 300211, China
| | - Juan Ma
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Qingfeng Fu
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, 300211, China
| | - Zhiwen Zheng
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, 300211, China
| | - E Du
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, 300211, China
| | - Yong Xu
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, 300211, China
| | - Zhihong Zhang
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, 300211, China.
| |
Collapse
|
111
|
Metallothionein 2A with Antioxidant and Antitumor Activity Is Upregulated by Caffeic Acid Phenethyl Ester in Human Bladder Carcinoma Cells. Antioxidants (Basel) 2022; 11:antiox11081509. [PMID: 36009228 PMCID: PMC9405133 DOI: 10.3390/antiox11081509] [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: 06/30/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/21/2022] Open
Abstract
Functions of metallothionein 2A (MT2A) in bladder cancer have not been extensively explored even though metallothioneins are regarded as modulators in several biological regulations including oxidation and cancerous development. We evaluated MT2A in bladder carcinoma cells in terms of the mechanisms of regulation and the underlying functions. MT2A overexpression not only downregulated endogenous ROS but also blocked ROS induced by H2O2. We used the annexin V-FITC apoptosis assay to determine the modulation of H2O2-induced cell apoptosis by MT2A expression. Results of immunoblot and reporter assays indicated that caffeic acid phenethyl ester (CAPE) treatment induced MT2A and heme oxygenase-1 (HO-1) expressions; moreover, the involvement of CAPE in either upregulation of the HO-1 expression or downregulation of endogenous ROS is MT2A dependent in bladder carcinoma cells. Knockdown of MT2A increased invasion and cell growth in vitro and in vivo, whereas ectopic overexpression of MT2A had the reverse effect in bladder carcinoma cells. Unlike bladder cancer tissues, the real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) analysis showed a significant level of MT2A mRNA in the normal bladder tissues. Collectively, our results indicated that MT2A is acting as an antioxidant and also a tumor suppressor in human bladder carcinoma cells.
Collapse
|
112
|
Bai Y, Chen D, Cheng C, Li Z, Chi H, Zhang Y, Zhang X, Tang S, Zhao Q, Ang B, Zhang Y. Immunosuppressive landscape in hepatocellular carcinoma revealed by single-cell sequencing. Front Immunol 2022; 13:950536. [PMID: 35967424 PMCID: PMC9365996 DOI: 10.3389/fimmu.2022.950536] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/05/2022] [Indexed: 12/18/2022] Open
Abstract
Background/Aims Hepatocellular carcinoma (HCC), accounting for 75-85% of primary liver cancer cases, is the third leading cause of cancer-related death worldwide. The purpose of this research was to examine the tumor immune microenvironment (TIME) in HCC. Methods We investigated the HCC TIME by integrated analysis of single-cell and bulk-tissue sequencing data to reveal the landscape of major immune cell types. Results Regulatory T(Treg) cells were found to be specifically distributed in the TIME of HCC. Several immune checkpoints, including TNFRSF4, TIGIT and CTLA4, were found to be uniquely overexpressed in Treg cells, and the glycolysis/gluconeogenesis pathway was enriched in Treg cells. We also discovered the presence of two NK-cell subsets with different cytotoxic capacities, one in an activated state with antitumor effects and another with an exhausted status. In addition, memory B cells in HCC were found to exist in a unique state, with high proliferation, low differentiation, and low activity, which was induced by overexpression of PRAP1 and activation of the MIF-CD74 axis. Conclusions We revealed the TIME landscape in HCC, highlighting the heterogeneity of major immune cell types and their potential mechanisms in the formation of an immunosuppressive environment. Hence, blocking the formation of the TIME could be a useful therapeutic strategy for HCC.
Collapse
Affiliation(s)
- Yi Bai
- Department of Hepatobiliary Surgery, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Dapeng Chen
- Tianjin First Central Hospital Clinic Institute, Tianjin Medical University, Tianjin, China
| | - Chuanliang Cheng
- Tianjin First Central Hospital Clinic Institute, School of Medicine, Nankai University, Tianjin, China
| | - Zhongmin Li
- Tianjin First Central Hospital Clinic Institute, Tianjin Medical University, Tianjin, China
| | - Hao Chi
- Tianjin First Central Hospital Clinic Institute, Tianjin Medical University, Tianjin, China
| | - Yuliang Zhang
- Tianjin First Central Hospital Clinic Institute, Tianjin Medical University, Tianjin, China
| | - Xiaoyu Zhang
- Tianjin First Central Hospital Clinic Institute, Tianjin Medical University, Tianjin, China
| | - Shaohai Tang
- Tianjin First Central Hospital Clinic Institute, Tianjin Medical University, Tianjin, China
| | - Qiang Zhao
- College of Life Sciences, Nankai University, Tianjin, China
| | - Bing Ang
- Oncology Department, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Yamin Zhang
- Department of Hepatobiliary Surgery, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
| |
Collapse
|
113
|
Azzarito G, Visentin M, Leeners B, Dubey RK. Transcriptomic and Functional Evidence for Differential Effects of MCF-7 Breast Cancer Cell-Secretome on Vascular and Lymphatic Endothelial Cell Growth. Int J Mol Sci 2022; 23:ijms23137192. [PMID: 35806196 PMCID: PMC9266834 DOI: 10.3390/ijms23137192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/16/2022] [Accepted: 06/24/2022] [Indexed: 01/14/2023] Open
Abstract
Vascular and lymphatic vessels drive breast cancer (BC) growth and metastasis. We assessed the cell growth (proliferation, migration, and capillary formation), gene-, and protein-expression profiles of Vascular Endothelial Cells (VECs) and Lymphatic Endothelial Cells (LECs) exposed to a conditioned medium (CM) from estrogen receptor-positive BC cells (MCF-7) in the presence or absence of Estradiol. We demonstrated that MCF-7-CM stimulated growth and capillary formation in VECs but inhibited LEC growth. Consistently, MCF-7-CM induced ERK1/2 and Akt phosphorylation in VECs and inhibited them in LECs. Gene expression analysis revealed that the LECs were overall (≈10-fold) more sensitive to MCF-7-CM exposure than VECs. Growth/angiogenesis and cell cycle pathways were upregulated in VECs but downregulated in LECs. An angiogenesis proteome array confirmed the upregulation of 23 pro-angiogenesis proteins in VECs. In LECs, the expression of genes related to ATP synthesis and the ATP content were reduced by MCF-7-CM, whereas MTHFD2 gene, involved in folate metabolism and immune evasion, was upregulated. The contrasting effect of MCF-7-CM on the growth of VECs and LECs was reversed by inhibiting the TGF-β signaling pathway. The effect of MCF-7-CM on VEC growth was also reversed by inhibiting the VEGF signaling pathway. In conclusion, BC secretome may facilitate cancer cell survival and tumor growth by simultaneously promoting vascular angiogenesis and inhibiting lymphatic growth. The differential effects of BC secretome on LECs and VECs may be of pathophysiological relevance in BC.
Collapse
Affiliation(s)
- Giovanna Azzarito
- Department of Reproductive Endocrinology, University Hospital Zurich, 8952 Schlieren, Switzerland; (G.A.); (B.L.)
| | - Michele Visentin
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland;
| | - Brigitte Leeners
- Department of Reproductive Endocrinology, University Hospital Zurich, 8952 Schlieren, Switzerland; (G.A.); (B.L.)
| | - Raghvendra K. Dubey
- Department of Reproductive Endocrinology, University Hospital Zurich, 8952 Schlieren, Switzerland; (G.A.); (B.L.)
- Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Correspondence:
| |
Collapse
|
114
|
Pan F, Lin X, Hao L, Wang T, Song H, Wang R. The Critical Role of Ferroptosis in Hepatocellular Carcinoma. Front Cell Dev Biol 2022; 10:882571. [PMID: 35800895 PMCID: PMC9255949 DOI: 10.3389/fcell.2022.882571] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/03/2022] [Indexed: 12/14/2022] Open
Abstract
Liver cancer is the sixth most frequently diagnosed cancer and the third dominant cause of cancer death worldwide. Ferroptosis is characterized as an iron-dependent form of regulated cell death, with accumulation of lipid peroxides to lethal amounts. Evidences have showed that ferroptosis is closely associated with HCC, but the mechanisms are still poorly understood. In this review, we mainly summarize the roles of several typical molecules as well as radiotherapy in regulating the ferroptosis process in HCC. Chances are that this review may help address specific issues in the treatment of HCC.
Collapse
|
115
|
Wu S, Pan R, Lu J, Wu X, Xie J, Tang H, Li X. Development and Verification of a Prognostic Ferroptosis-Related Gene Model in Triple-Negative Breast Cancer. Front Oncol 2022; 12:896927. [PMID: 35719954 PMCID: PMC9202593 DOI: 10.3389/fonc.2022.896927] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/02/2022] [Indexed: 11/14/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is the subtype with the worst prognosis of breast cancer. Ferroptosis, a novel iron-dependent programmed cell death, has an increasingly important role in tumorigenesis and development. However, there is still a lack of research on the relationship between ferroptosis-related genes and the prognosis of TNBC. In this study, we obtained the gene expression profile of TNBC patients and matched clinical data from The Cancer Genome Atlas (TCGA) database. Univariate Cox analysis was used to screen out ferroptosis-related genes associated with TNBC prognosis. Then, the least absolute shrinkage and selection operator (LASSO) regression analysis was employed to establish a prognostic prediction model. A 15-ferroptosis-related gene prognostic prediction model was developed, which classified patients into low-risk (LR) or high-risk (HR) groups. Kaplan-Meier analysis results showed that the prognosis of the LR group was better. The receiver operating characteristic (ROC) curve also confirmed the satisfactory predictive ability of this model. Evaluation of the immune microenvironment of TNBC patients in the HR and LR group suggested these 15 ferroptosis-related genes might affect the prognosis of TNBC by regulating the tumor microenvironment. Our prognostic model can provide a theoretical basis for accurate prognosis prediction of TNBC in clinical practice.
Collapse
Affiliation(s)
- Song Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ruilin Pan
- Department of Breast Surgery, The First People's Hospital of Foshan, Foshan, China
| | - Jibu Lu
- Department of Breast Surgery, The First People's Hospital of Foshan, Foshan, China
| | - Xiaoling Wu
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Jingdong Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Hailin Tang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xing Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| |
Collapse
|
116
|
Rye MB, Krossa S, Hall M, van Mourik C, Bathen TF, Drabløs F, Tessem MB, Bertilsson H. The genes controlling normal function of citrate and spermine secretion are lost in aggressive prostate cancer and prostate model systems. iScience 2022; 25:104451. [PMID: 35707723 PMCID: PMC9189124 DOI: 10.1016/j.isci.2022.104451] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/12/2022] [Accepted: 05/17/2022] [Indexed: 11/22/2022] Open
Abstract
High secretion of the metabolites citrate and spermine is a unique hallmark for normal prostate epithelial cells, and is reduced in aggressive prostate cancer. However, the identity of the genes controlling this biological process is mostly unknown. In this study, we have created a gene signature of 150 genes connected to citrate and spermine secretion in the prostate. We have computationally integrated metabolic measurements with multiple transcriptomics datasets from the public domain, including 3826 tissue samples from prostate and prostate cancer. The accuracy of the signature is validated by its unique enrichment in prostate samples and prostate epithelial tissue compartments. The signature highlights genes AZGP1, ANPEP and metallothioneins with zinc-binding properties not previously studied in the prostate, and the expression of these genes are reduced in more aggressive cancer lesions. However, the absence of signature enrichment in common prostate model systems can make it challenging to study these genes mechanistically. Novel 150 gene signature reflecting prostatic citrate and spermine secretion Identified several zinc-binding proteins not previously investigated in the prostate The signature is absent in prostate model systems
Collapse
Affiliation(s)
- Morten Beck Rye
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, P.O. Box 8905, 7491 Trondheim, Norway.,Clinic of Surgery, St.Olavs Hospital, Trondheim University Hospital, 7030 Trondheim, Norway.,Clinic of Laboratory Medicine, St.Olavs Hospital, Trondheim University Hospital, 7030 Trondheim, Norway.,BioCore - Bioinformatics Core Facility, NTNU - Norwegian University of Science and Technology, P.O. Box 8905, 7491 Trondheim, Norway
| | - Sebastian Krossa
- Department of Circulation and Medical Imaging, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Martina Hall
- Department of Biotechnology and Food Science, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,K. G. Jebsen Center for Genetic Epidemiology, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Casper van Mourik
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, P.O. Box 8905, 7491 Trondheim, Norway.,Institute for Life Science & Technology, Hanze University of Applied Sciences, 9747 AS Groningen, the Netherlands
| | - Tone F Bathen
- Department of Circulation and Medical Imaging, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Finn Drabløs
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, P.O. Box 8905, 7491 Trondheim, Norway
| | - May-Britt Tessem
- Clinic of Surgery, St.Olavs Hospital, Trondheim University Hospital, 7030 Trondheim, Norway.,Department of Circulation and Medical Imaging, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Helena Bertilsson
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, P.O. Box 8905, 7491 Trondheim, Norway.,Clinic of Surgery, St.Olavs Hospital, Trondheim University Hospital, 7030 Trondheim, Norway
| |
Collapse
|
117
|
Identification of ferroptosis-related genes for overall survival prediction in hepatocellular carcinoma. Sci Rep 2022; 12:10007. [PMID: 35705729 PMCID: PMC9200861 DOI: 10.1038/s41598-022-14554-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/08/2022] [Indexed: 12/24/2022] Open
Abstract
Ferroptosis is a novel type of cell death depending on iron and is strongly related to the development of tumors. Hepatocellular carcinoma (HCC) is a malignancy with high incidence. Despite some reports demonstrating the relation between ferroptosis-related genes and HCC, more details have not been excavated. In the present study, we collected and analyzed HCC patients' datasets from the TCGA-LIHC project and ICGC portal, respectively. Through the bioinformatic methods, we screened 126 differentially expressed genes. Then a prognostic model was established with four genes (GPX2, MT3, PRDX1, and SRXN1). PRDX1 is the hub gene of the prognosis model and has a high expression in hepatocellular carcinoma tumor tissue and cell lines. We further found that silencing PRDX1 increased the accumulation of ferrous ions and lipid peroxidation accumulation in HEPG2 cells and promoted ferroptosis in hepatocellular carcinoma. In conclusion, the study demonstrated the four-gene signature can be used to predict HCC prognosis. It also revealed the potential function of the ferroptosis-related gene PRDX1 in HCC, which can be a biomarker of the prediction for HCC outcome.
Collapse
|
118
|
Ang GCK, Gupta A, Surana U, Yap SXL, Taneja R. Potential Therapeutics Targeting Upstream Regulators and Interactors of EHMT1/2. Cancers (Basel) 2022; 14:cancers14122855. [PMID: 35740522 PMCID: PMC9221123 DOI: 10.3390/cancers14122855] [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: 05/23/2022] [Revised: 06/07/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The expression of Euchromatin histone lysine methyltransferase 1 and 2 (EHMT1/2) is deregulated in many cancers. Most studies thus far have focused on the downstream targets and pathways regulated by EHMTs. However, the mechanisms that lead to their deregulated expression, and the interacting proteins that could impact EHMT activity are not well understood. In this review, we summarize our current understanding of the upstream regulators and the interactors that provide alternative therapeutic approaches to tackle EHMT driven malignancies. Abstract Euchromatin histone lysine methyltransferases (EHMTs) are epigenetic regulators responsible for silencing gene transcription by catalyzing H3K9 dimethylation. Dysregulation of EHMT1/2 has been reported in multiple cancers and is associated with poor clinical outcomes. Although substantial insights have been gleaned into the downstream targets and pathways regulated by EHMT1/2, few studies have uncovered mechanisms responsible for their dysregulated expression. Moreover, EHMT1/2 interacting partners, which can influence their function and, therefore, the expression of target genes, have not been extensively explored. As none of the currently available EHMT inhibitors have made it past clinical trials, understanding upstream regulators and EHMT protein complexes may provide unique insights into novel therapeutic avenues in EHMT-overexpressing cancers. Here, we review our current understanding of the regulators and interacting partners of EHMTs. We also discuss available therapeutic drugs that target the upstream regulators and binding partners of EHMTs and could potentially modulate EHMT function in cancer progression.
Collapse
Affiliation(s)
- Gareth Chin Khye Ang
- Healthy Longevity Translational Research Program, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore; (G.C.K.A.); (A.G.)
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore;
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research A*STAR, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Amogh Gupta
- Healthy Longevity Translational Research Program, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore; (G.C.K.A.); (A.G.)
| | - Uttam Surana
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore;
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research A*STAR, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Shirlyn Xue Ling Yap
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
| | - Reshma Taneja
- Healthy Longevity Translational Research Program, Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore; (G.C.K.A.); (A.G.)
- Correspondence: ; Tel.: +65-(65)-153-236; Fax: +65-(67)-788-161
| |
Collapse
|
119
|
Wei S, Yu X, Wen X, Zhang M, Lang Q, Zhong P, Huang B. Genetic Variations in Metallothionein Genes and Susceptibility to Hypertensive Disorders of Pregnancy: A Case-Control Study. Front Genet 2022; 13:830446. [PMID: 35734434 PMCID: PMC9208279 DOI: 10.3389/fgene.2022.830446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/19/2022] [Indexed: 01/07/2023] Open
Abstract
Background: The involvement of oxidative stress in the pathological process of hypertensive disorders of pregnancy (HDP) gives rise to the interest in exploring the association of genetic variations in antioxidant metallothionein (MT) genes with HDP susceptibility. Methods: Seventeen single-nucleotide polymorphisms(SNPs) in MT genes were selected to conduct genotyping based on a case-control study consisting of 371 HDP cases (pregnancy with chronic hypertension (66), gestational hypertension (172), and preeclampsia or preeclampsia superimposed on chronic hypertension (133)) and 479 controls. The association between SNPs in MTs and the risk of HDP was estimated with unconditional logistic regression analysis and further tested with the false-positive report probability (FPRP) procedure. The joint effects of SNPs on the HDP risk were assessed by haplotype analysis. Results: After the adjustment for age and pre-pregnancy body mass index (pre-BMI) in the logistic regress analysis and followed by the FPRP test, the genetic variation rs10636 (OR = 0.46, 95% CI: 0.30–0.71 for GG vs. CC, p = 0.000 and OR = 0.48, 95% CI: 0.32–0.73 for GG vs. CG/CC, p = 0.001) in MT2A was associated with gestational hypertension. Other four SNPs, that is, rs11076161 (OR = 1.89, 95% CI: 1.35–2.63 for GG vs. GA/AA, p = 0.000) in MT1A; rs7191779 (OR = 1.54, 95% CI: 1.11–2.13 for CC vs. CG/GG, p = 0.010) in MT1B; rs8044719 (OR = 0.57, 95% CI: 0.40–0.80 for GT vs. GG, p = 0.001) in MT1DP; and rs8052334 (OR = 1.52, 95% CI: 1.10–2.11 for TT vs. TC/CC, p = 0.012) in MT1B were significantly associated with the susceptibility of HDP. The haplotype analysis among 11, 10, 10, and seven SNPs in MT (MT1A, MT2A, MT1M, MT1B, and MT1DP) genes showed that eight (A-C-G-T-C-G-A-G-C-G-C, OR = 4.559; A-C-T-C-C-C-A-G-C-G-C, OR = 5.777; A-C-T-T-C-G-A-G-C-G-C, OR = 4.590; G-A-T-C-C-G-C-G-G-C-C, OR = 4.065; G-A-T-C-G-C-C-G-G-C-C, OR = 4.652; G-A-T-T-C-C-C-G-G-C-C, OR = 0.404; G-C-T-C-C-C-A-G-G-C-C, OR = 1.901; G-C-T-T-C-C-A-G-G-C-C, and OR = 3.810), five (C-G-A-T-C-A-C-C-G-G, OR = 2.032; C-G-A-T-C-G-C-C-G-G, OR = 2.077; G-A-C-T-C-A-C-C-T-G, OR = 0.564; G-G-A-G-C-A-C-C-G-G, OR = 5.466; G-G-A-T-T-A-G-C-G-G, and OR = 0.284), five (A-C-G-T-C-G-A-G-C-C, OR = 2.399; A-C-T-C-C-C-C-T-G-G, OR = 0.259; G-A-T-C-C-C-C-G-G-C, OR = 1.572; G-A-T-C-G-C-C-G-G-C, OR = 0.001; G-C-T-C-G-C-A-G-G-C, and OR = 2.512), and five (A-C-T-C-C-C-G, OR = 0.634; G-A-G-C-C-C-G, OR = 4.047; G-A-T-T-G-C-G, OR = 0.499; G-C-G-T-C-A-G, and OR = 7.299; G-C-T-C-C-A-G, OR = 1.434) haplotypes were significantly associated with pregnancy with chronic hypertension, gestational hypertension, preeclampsia, or preeclampsia superimposed on chronic hypertension and HDP. Conclusion: These variant MT alleles and their combination patterns may be used as genetic markers for predicting HDP susceptibility.
Collapse
Affiliation(s)
- Shudan Wei
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, Guilin Medical University, Guilin, China
| | - Xiangyuan Yu
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, Guilin Medical University, Guilin, China
| | - Xiaolan Wen
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, Guilin Medical University, Guilin, China
| | - Min Zhang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, Guilin Medical University, Guilin, China
| | - Qi Lang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, Guilin Medical University, Guilin, China
| | - Ping Zhong
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Bo Huang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, Guilin Medical University, Guilin, China
- *Correspondence: Bo Huang,
| |
Collapse
|
120
|
Barman SK, Zaman MS, Veljanoski F, Malladi CS, Mahns DA, Wu MJ. Expression profiles of the genes associated with zinc homeostasis in normal and cancerous breast and prostate cells. Metallomics 2022; 14:6601457. [PMID: 35657662 DOI: 10.1093/mtomcs/mfac038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/12/2022] [Indexed: 11/14/2022]
Abstract
Zn2+ dyshomeostasis is an intriguing phenomenon in breast and prostate cancers, with breast cancer cells exhibiting higher intracellular Zn2+ level compared to their corresponding normal epithelial cells, in contrast to the low Zn2+ level in prostate cancer cells. In order to gain molecular insights into the zinc homeostasis of breast and prostate cancer cells, this study profiled the expression of 28 genes, including 14 zinc importer genes (SLC39A1-14) which encode ZIP1-14 to transport Zn2+ into the cytoplasm, 10 zinc exporter genes (SLC30A1-10) which encode ZnT1-10 to transport Zn2+ out of the cytoplasm and 4 metallothionein genes (MT1B, MT1F, MT1X, MT2A) in breast (MCF10A, MCF-7, MDA-MB-231) and prostate (RWPE-1, PC3, DU145) cell lines in response to extracellular zinc exposures at a mild cytotoxic dosage and a benign dosage. The RNA samples were prepared at 0 min (T0), 30 min (T30) and 120 min (T120) in a time course with or without zinc exposure, which were used for profiling the baseline and dynamic gene expression. The up-regulation of MT genes was observed across the breast and prostate cancer cell lines. The expression landscape of SLC39A and SLC30A was revealed by the qRT-PCR data of this study, which sheds light on the divergence of intracellular Zn2+ levels for breast and prostate cancer cells. Taken together, the findings are valuable in unravelling the molecular intricacy of zinc homeostasis in breast and prostate cancer cells.
Collapse
Affiliation(s)
- Shital K Barman
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751
| | - Mohammad S Zaman
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751
| | - Filip Veljanoski
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751
| | - Chandra S Malladi
- Proteomics and Lipidomics Lab, School of Medicine, Western Sydney University, Locked
| | - David A Mahns
- School of Medicine, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751
| | - Ming J Wu
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751
| |
Collapse
|
121
|
Overexpression of long non-coding RNA ACTA2-AS1 inhibits the viability, proliferation, migration and invasion of colorectal cancer cells. Tissue Cell 2022; 76:101769. [DOI: 10.1016/j.tice.2022.101769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 02/25/2022] [Accepted: 02/25/2022] [Indexed: 11/21/2022]
|
122
|
Liu X, Quan J, Shen Z, Zhang Z, Chen Z, Li L, Li X, Hu G, Deng X. Metallothionein 2A (MT2A) controls cell proliferation and liver metastasis by controlling the MST1/LATS2/YAP1 signaling pathway in colorectal cancer. Cancer Cell Int 2022; 22:205. [PMID: 35642057 PMCID: PMC9158144 DOI: 10.1186/s12935-022-02623-w] [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: 12/18/2021] [Accepted: 05/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the three major cancers in the world and is the cancer with the most liver metastasis. The present study aimed to investigate the role of metallothionein 2A (MT2A) in the modulation of CRC cell proliferation and liver metastasis, as well as its molecular mechanisms. METHODS The expression profile of metallothionein 2A (MT2A) in colorectal cancer retrieved from TCGA, GEO and Oncomine database. The biological effect of MT2A overexpression was investigated mainly involving cell proliferation and migration in CRC cells as well as growth and metastasis in CRC animal models. To explore the specific mechanism of MT2A metastasis in CRC, transcriptome sequencing was used to compare the overall expression difference between the control group and the MT2A overexpression group. RESULTS Metallothionein 2A (MT2A) was downregulated in the tumor tissues of patients with CRC compared to adjacent normal tissues and was related to the tumor M stage of patients. MT2A overexpression inhibited CRC cell proliferation and migration in cells, as well as growth and metastasis in CRC animal models. While knockdown of MT2A had the opposite effect in cells. Western blotting confirmed that MT2A overexpression promoted the phosphorylation of MST1, LAST2 and YAP1, thereby inhibiting the Hippo signaling pathway. Additionally, specific inhibitors of MST1/2 inhibited MT2A overexpression-mediated phosphorylation and relieved the inhibition of the Hippo signaling pathway, thus promoting cell proliferation. Immunohistochemistry in subcutaneous grafts and liver metastases further confirmed this result. CONCLUSIONS Our results suggested that MT2A is involved in CRC growth and liver metastasis. Therefore, MT2A and MST1 may be potential therapeutic targets for patients with CRC, especially those with liver metastases.
Collapse
Affiliation(s)
- Xi Liu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Jun Quan
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Zhaolong Shen
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Zequn Zhang
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China.
| | - Zhijian Chen
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Liang Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Xiaorong Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Gui Hu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Tongzipo Road, Changsha, 410013, Hunan, People's Republic of China
| | - Xiaofeng Deng
- Department of General Surgery, The Second Xiangya Hospital of Central South University, Renmin Road, Changsha, 410000, Hunan, People's Republic of China.
| |
Collapse
|
123
|
Xiao J, McGill JR, Nasir A, Lekan A, Johnson B, Wilkins DJ, Pearson GW, Tanner K, Goodarzi H, Glasgow E, Schlegel R, Agarwal S. Identifying drivers of breast cancer metastasis in progressively invasive subpopulations of zebrafish-xenografted MDA-MB-231. MOLECULAR BIOMEDICINE 2022; 3:16. [PMID: 35614362 PMCID: PMC9133282 DOI: 10.1186/s43556-022-00080-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/09/2022] [Indexed: 12/03/2022] Open
Abstract
Cancer metastasis is the primary cause of the high mortality rate among human cancers. Efforts to identify therapeutic agents targeting cancer metastasis frequently fail to demonstrate efficacy in clinical trials despite strong preclinical evidence. Until recently, most preclinical studies used mouse models to evaluate anti-metastatic agents. Mouse models are time-consuming and expensive. In addition, an important drawback is that mouse models inadequately model the early stages of metastasis which plausibly leads to the poor correlation with clinical outcomes. Here, we report an in vivo model based on xenografted zebrafish embryos where we select for progressively invasive subpopulations of MDA-MB-231 breast cancer cells. A subpopulation analogous to circulating tumor cells found in human cancers was selected by injection of MDA-MB-231 cells into the yolk sacs of 2 days post-fertilized zebrafish embryos and selecting cells that migrated to the tail. The selected subpopulation derived from MDA-MB-231 cells were increasingly invasive in zebrafish. Isolation of these subpopulations and propagation in vitro revealed morphological changes consistent with activation of an epithelial-mesenchymal transition program. Differential gene analysis and knockdown of genes identified gene-candidates (DDIT4, MT1X, CTSD, and SERPINE1) as potential targets for anti-metastasis therapeutics. Furthermore, RNA-splicing analysis reinforced the importance of BIRC5 splice variants in breast cancer metastasis. This is the first report using zebrafish to isolate and expand progressively invasive populations of human cancer cells. The model has potential applications in understanding the metastatic process, identification and/or development of therapeutics that specifically target metastatic cells and formulating personalized treatment strategies for individual cancer patients.
Collapse
Affiliation(s)
- Jerry Xiao
- Department of Pathology, Center for Cell Reprogramming, Georgetown University, Washington, DC, USA.,Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Joseph R McGill
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Apsra Nasir
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Alexander Lekan
- Department of Pathology, Center for Cell Reprogramming, Georgetown University, Washington, DC, USA
| | - Bailey Johnson
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Devan J Wilkins
- Department of Pathology, Center for Cell Reprogramming, Georgetown University, Washington, DC, USA.,Eastern Virginia Medical School, Norfolk, VA, USA
| | - Gray W Pearson
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Kandice Tanner
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Eric Glasgow
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Richard Schlegel
- Department of Pathology, Center for Cell Reprogramming, Georgetown University, Washington, DC, USA
| | - Seema Agarwal
- Department of Pathology, Center for Cell Reprogramming, Georgetown University, Washington, DC, USA.
| |
Collapse
|
124
|
Mao W, Pouyan MB, Kostka D, Chikina M. Non-negative Independent Factor Analysis disentangles discrete and continuous sources of variation in scRNA-seq data. Bioinformatics 2022; 38:2749-2756. [PMID: 35561207 PMCID: PMC9113312 DOI: 10.1093/bioinformatics/btac136] [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: 03/22/2021] [Revised: 02/25/2022] [Accepted: 03/17/2022] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Single-cell RNA-seq analysis has emerged as a powerful tool for understanding inter-cellular heterogeneity. Due to the inherent noise of the data, computational techniques often rely on dimensionality reduction (DR) as both a pre-processing step and an analysis tool. Ideally, DR should preserve the biological information while discarding the noise. However, if the DR is to be used directly to gain biological insight it must also be interpretable-that is the individual dimensions of the reduction should correspond to specific biological variables such as cell-type identity or pathway activity. Maximizing biological interpretability necessitates making assumption about the data structures and the choice of the model is critical. RESULTS We present a new probabilistic single-cell factor analysis model, Non-negative Independent Factor Analysis (NIFA), that incorporates different interpretability inducing assumptions into a single modeling framework. The key advantage of our NIFA model is that it simultaneously models uni- and multi-modal latent factors, and thus isolates discrete cell-type identity and continuous pathway activity into separate components. We apply our approach to a range of datasets where cell-type identity is known, and we show that NIFA-derived factors outperform results from ICA, PCA, NMF and scCoGAPS (an NMF method designed for single-cell data) in terms of disentangling biological sources of variation. Studying an immunotherapy dataset in detail, we show that NIFA is able to reproduce and refine previous findings in a single analysis framework and enables the discovery of new clinically relevant cell states. AVAILABILITY AND IMPLEMENTATION NFIA is a R package which is freely available at GitHub (https://github.com/wgmao/NIFA). The test dataset is archived at https://zenodo.org/record/6286646. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Weiguang Mao
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Joint Carnegie Mellon-University of Pittsburgh Ph.D. Program in Computational Biology, Pittsburgh, PA 15260, USA
| | | | - Dennis Kostka
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Joint Carnegie Mellon-University of Pittsburgh Ph.D. Program in Computational Biology, Pittsburgh, PA 15260, USA
- Department of Developmental Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | | |
Collapse
|
125
|
Chen CW, Huang NK, Lee YL, Fan CK, Chen YC, Liu CW, Huang HM. Activin A downregulates the CD69-MT2A axis via p38MAPK to induce erythroid differentiation that sensitizes BCR-ABL-positive cells to imatinib. Exp Cell Res 2022; 417:113219. [DOI: 10.1016/j.yexcr.2022.113219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/25/2022] [Accepted: 05/19/2022] [Indexed: 11/04/2022]
|
126
|
Alsagaby SA. Transcriptomics-Based Investigation of Molecular Mechanisms Underlying Apoptosis Induced by ZnO Nanoparticles in Human Diffuse Large B-Cell Lymphoma. Int J Nanomedicine 2022; 17:2261-2281. [PMID: 35611214 PMCID: PMC9124502 DOI: 10.2147/ijn.s355408] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/29/2022] [Indexed: 12/13/2022] Open
Abstract
Introduction Zinc oxide nanoparticles (ZnO NPs) show anti-cancer activity. Diffuse Large B-cell Lymphoma (DLBCL) is a type of B-cell malignancies with unsatisfying treatment outcomes. This study was set to assess the potential of ZnO NPs to selectively induce apoptosis in human DLBCL cells (OCI-LY3), and to describe possible molecular mechanisms of action. Methods The impact of ZnO NPs on DLBCL cells and normal peripheral blood mononuclear cells (PBMCs) was studied using cytotoxicity assay and flow-cytometry. Transcriptomics analysis was conducted to identify ZnO NPs-dependent changes in the transcriptomic profiles of DLBCL cells. Results ZnO NPs selectively induced apoptosis in DLBCL cells, and caused changes in their transcriptomes. Deferential gene expression (DGE) with fold change (FC) ≥3 and p ≤ 0.008 with corrected p ≤ 0.05 was identified for 528 genes; 125 genes were over-expressed and 403 genes were under-expressed in ZnO NPs-treated DLBCL cells. The over-expressed genes involved in biological processes and pathways like stress response to metal ion, cellular response to zinc ion, metallothioneins bind metals, oxidative stress, and negative regulation of growth. In contrast, the under-expressed genes were implicated in DNA packaging complex, signaling by NOTCH, negative regulation of gene expression by epigenetic, signaling by WNT, M phase of cell cycle, and telomere maintenance. Setting the FC to ≥1.5 with p ≤ 0.05 and corrected p ≤ 0.1 showed ZnO NPs to induce over-expression of anti-oxidant genes and under-expression of oncogenes; target B-cell receptor (BCR) signaling pathway and NF-κB pathway; and promote apoptosis by intrinsic and extrinsic pathways. Discussion Overall, ZnO NPs selectively induced apoptosis in DLBCL cells, and possible molecular mechanisms of action were described.
Collapse
Affiliation(s)
- Suliman A Alsagaby
- Department of Medical Laboratories Sciences, College of Applied Medical Sciences, Majmaah University, AL-Majmaah, 11932, Saudi Arabia
- Correspondence: Suliman A Alsagaby, Email
| |
Collapse
|
127
|
Peng B, Peng J, Kang F, Zhang W, Peng E, He Q. Ferroptosis-Related Gene MT1G as a Novel Biomarker Correlated With Prognosis and Immune Infiltration in Colorectal Cancer. Front Cell Dev Biol 2022; 10:881447. [PMID: 35517502 PMCID: PMC9065264 DOI: 10.3389/fcell.2022.881447] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/22/2022] [Indexed: 12/13/2022] Open
Abstract
Ferroptosis, a newly discovered way of cell death, has been proved to be involved in the oncogenesis and development of cancers, including colorectal cancer (CRC). Here, by identifying the differentially expressed genes (DEGs) from three CRC transcriptome microarray datasets (GSE20842, GSE23878, and GSE25070), we found that the expression of MT1G was significantly decreased in CRC tissues, and the patients with a high level of MT1G displayed a poor prognosis. Quantitative PCR (qPCR) further confirmed the downregulated MT1G in two CRC cells, HCT8 and HCT116. The colony-forming assay indicated that the MT1G overexpression exhibited a remarkable inhibition of cell proliferation in HCT8 and HCT116 cells. In addition, we explored the co-expressed genes of MT1G to gain a better understanding of its potential signaling pathways. Aberrantly expressed MT1G also affected the immune response of CRC patients. Collectively, these findings might deepen our comprehension on the potential biological implications of MT1G in CRC.
Collapse
Affiliation(s)
- Bi Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Jinwu Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
- Department of Pathology, Xiangya Changde Hospital, Changde, China
- *Correspondence: Qingchun He, ; Jinwu Peng,
| | - Fanhua Kang
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Wenqin Zhang
- Department of Pathology, Xiangya Changde Hospital, Changde, China
| | - Emin Peng
- Xiangya International Medical Center, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Qingchun He
- Department of Emergency, Xiangya Hospital, Central South University, Changsha, China
- Department of Emergency, Xiangya Changde Hospital, Changde, China
- *Correspondence: Qingchun He, ; Jinwu Peng,
| |
Collapse
|
128
|
Structural Characterization and In Vitro Antioxidant Activity of Metallothionein from Oratosquilla oratoria. Molecules 2022; 27:molecules27072320. [PMID: 35408719 PMCID: PMC9000697 DOI: 10.3390/molecules27072320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 02/01/2023] Open
Abstract
We report here the purification of a novel metal-binding protein from Oratosquilla oratoria (O. oratoria MT-1) by gel and ion-exchange chromatography. SDS-PAGE and MALDI-TOF analyses demonstrated that isolated O. oratoria MT-1 was of high purity with a molecular weight of 12.4 kDa. The fluorescence response to SBD-F derivatives revealed that O. oratoria MT-1 contained a large number of sulfhydryl groups, which is a general property of metallothioneins. Zn and Cu metal stoichiometries for O. oratoria MT-1 were 3.97:1 and 0.55:1, respectively. The proportion of cysteine (Cys) residues in the amino acid composition was 32.69%, and aromatic amino acids were absent. The peptide sequence coverage with Macrobrachium rosenbergii calmodulin (accession AOA3S8FSK5) was 60%. Infrared spectroscopy of O. oratoria MT-1 revealed two obvious peaks at absorption frequencies for the amide I band and the amide II band. CD spectra revealed that the secondary structure was mainly composed of random coil (57.6%) and β-sheet (39.9%). An evaluation of in vitro antioxidant activity revealed that isolated O. oratoria MT-1 has strong reducing activities, exhibiting scavenging rates for DPPH and OH of 77.8% and 75.8%, respectively (IC50 values 0.57 mg/mL and 1.1 mg/mL). O. oratoria MT-1 may be used as a functional additive in cosmetics, health foods, and medical products, as well as a reference material for quantitative analysis of metallothionein in such products.
Collapse
|
129
|
Identification of Potential Diagnostic Biomarkers and Biological Pathways in Hypertrophic Cardiomyopathy Based on Bioinformatics Analysis. Genes (Basel) 2022; 13:genes13030530. [PMID: 35328083 PMCID: PMC8951232 DOI: 10.3390/genes13030530] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/10/2022] [Accepted: 03/14/2022] [Indexed: 12/13/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is a genetic heterogeneous disorder and the main cause of sudden cardiac death in adolescents and young adults. This study was aimed at identifying potential diagnostic biomarkers and biological pathways to help to diagnose and treat HCM through bioinformatics analysis. We selected the GSE36961 dataset from the Gene Expression Omnibus (GEO) database and identified 893 differentially expressed genes (DEGs). Subsequently, 12 modules were generated through weighted gene coexpression network analysis (WGCNA), and the turquoise module showed the highest negative correlation with HCM (cor = −0.9, p-value = 4 × 10−52). With the filtering standard gene significance (GS) < −0.7 and module membership (MM) > 0.9, 19 genes were then selected to establish the least absolute shrinkage and selection operator (LASSO) model, and LYVE1, MAFB, and MT1M were finally identified as key genes. The expression levels of these genes were additionally verified in the GSE130036 dataset. Gene Set Enrichment Analysis (GSEA) showed oxidative phosphorylation, tumor necrosis factor alpha-nuclear factor-κB (TNFα-NFκB), interferon-gamma (IFNγ) response, and inflammatory response were four pathways possibly related to HCM. In conclusion, LYVE1, MAFB, and MT1M were potential biomarkers of HCM, and oxidative stress, immune response as well as inflammatory response were likely to be associated with the pathogenesis of HCM.
Collapse
|
130
|
Chen L, Wang C, Wang Y, Hong T, Zhang G, Cui X. Functions, Roles, and Biological Processes of Ferroptosis-Related Genes in Renal Cancer: A Pan-Renal Cancer Analysis. Front Oncol 2022; 11:697697. [PMID: 35360452 PMCID: PMC8962645 DOI: 10.3389/fonc.2021.697697] [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: 04/20/2021] [Accepted: 12/13/2021] [Indexed: 12/02/2022] Open
Abstract
Ferroptosis is a cell death process discovered in recent years, highly related to cancer, acute kidney injury, and other diseases. In this study, a pan-renal cancer analysis of ferroptosis-associated genes in renal cancer was performed to construct a multigene joint signature for predicting prognosis in renal cancer patients. First, gene expression profiles were downloaded from the TCGA and GTEx databases to search for genes significantly associated with renal cancer prognosis through differential gene expression analysis, weighted gene co-expression network analysis (WGCNA), and survival analysis. Thereafter, the gene-set enrichment analysis (GSEA) was used to identify the biological processes in which ferroptosis-associated genes might be involved. Weighted gene co-expression network analysis resulted in 4,434 differentially expressed genes (DEGs) and 42 co-expression modules, among which ferroptosis-related genes were distributed in 11 gene modules. The survival analysis screening resulted in three DEGs associated with renal cancer prognosis, namely SLC7A11, HMOX1, and MT1G. Specifically, SLC7A11 and HMOX1 were upregulated in renal cancer tissues, while MT1G was downregulated. Receiver operating characteristic (ROC) curves, combined with Kaplan–Meier and Cox regression analysis, revealed that high expression of SLC7A11 was a prognostic risk factor for four different renal cancers, that low expression of HMOX1 was a poor prognostic marker for patients, and that increased expression of MT1G increased the prognostic risk for three additional classes of renal cancer patients, except for renal papillary cell carcinoma. The GSEA results showed that the ferroptosis-related genes from these screens were mainly associated with signaling pathways related to tumor progression and tumor immunity. This study provides potential biological markers for prognosis prediction in renal cancer patients with different subtypes, and these results imply that ferroptosis is highly associated with renal carcinogenesis progression.
Collapse
Affiliation(s)
- Linbao Chen
- Department of Urinary Surgery, The Second Affiliated Hospital of Ningxia Medical University (The First People’s Hospital of Yinchuan), Yinchuan, China
- Ningxia Medical University, Yinchuan, China
- Department of Urinary Surgery, Postgraduate Training Base in Shanghai Gongli Hospital, Ningxia Medical University, Yinchuan, China
| | - Chao Wang
- Department of Urinary Surgery, Gongli Hospital, Second Military Medical University (Naval Medical University), Shanghai, China
- Department of Urology, The Affiliated Changzhou No. 2 People’s Hospital of Nanjing Medical University, Changzhou, China
| | - Yuning Wang
- Department of Urinary Surgery, Gongli Hospital, Second Military Medical University (Naval Medical University), Shanghai, China
| | - Tianyu Hong
- Department of Urinary Surgery, Gongli Hospital, Second Military Medical University (Naval Medical University), Shanghai, China
| | - Guangwen Zhang
- Department of Urinary Surgery, The Second Affiliated Hospital of Ningxia Medical University (The First People’s Hospital of Yinchuan), Yinchuan, China
- *Correspondence: Guangwen Zhang, ; Xingang Cui,
| | - Xingang Cui
- Department of Urinary Surgery, Gongli Hospital, Second Military Medical University (Naval Medical University), Shanghai, China
- Department of Urinary Surgery, Xinhua Hospital Affiliated To Shanghai Jiaotong University School of Medicine, Shanghai, China
- *Correspondence: Guangwen Zhang, ; Xingang Cui,
| |
Collapse
|
131
|
Jia E, Ren N, Guo B, Cui Z, Zhang B, Xue J. Construction and validation of a novel prognostic model for lung squamous cell cancer based on N6-methyladenosine-related genes. World J Surg Oncol 2022; 20:59. [PMID: 35220962 PMCID: PMC8883700 DOI: 10.1186/s12957-022-02509-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/01/2022] [Indexed: 12/24/2022] Open
Abstract
Background N6-methyladenosine (m6A) is the most prevalent modification in mRNA in biological processes and associated with various malignant tumor initiation and progression. The present study aimed to construct a prognostic risk model based on m6A-related genes (the downstream genes influenced by m6A modulators) for LUSC. Methods Based on TCGA, we stratified LUSC patients with and without genetic alteration of m6A modulators into altered and unaltered groups. Using univariate Cox and Lasso regression analyses, we identified prognostic m6A-related genes to construct a prognostic risk model. We then applied a multivariate Cox proportional regression model and the survival analysis to evaluate the risk model. Moreover, we performed the Receiver operating characteristic curve to assess the efficiency of the prognostic model based on TCGA and GSE43131. We analyzed the characteristics of tumor-associated immune cell infiltration in LUSC through the CIBERSORT method. Results Three m6A-related genes (FAM71F1, MT1E, and MYEOV) were identified as prognostic genes for LUSC. A novel prognostic risk model based on the three m6A-related genes was constructed. The multivariate Cox analysis showed that the prognostic risk model was an independent risk factor (HR = 2.44, 95% CI = 1.21~3.56, p = 0.029). Patients with a high-risk group had worse overall survival both in TCGA (p = 0.018) and GSE43131 (p = 0.00017). The 1, 2, and 3-year AUC value in TCGA was 0.662, 0.662, and 0.655, respectively; The 1, 2, and 3-year AUC value in GSE43131 was 0.724, 0.724, and 0.722, respectively. The proportion of infiltrated neutrophils in the high-risk group was higher than that in the low-risk group (p = 0.028), whereas that of resting NK cells (p = 0.002) was lower. Conclusion A novel prognostic risk model based on three m6A-related genes for LUSC was generated in this study. Supplementary Information The online version contains supplementary material available at 10.1186/s12957-022-02509-1.
Collapse
|
132
|
Abstract
Zn2+ ions are essential in many physiological processes, including enzyme catalysis, protein structural stabilization, and the regulation of many proteins. The affinities of proteins for Zn2+ ions span several orders of magnitude, with catalytic Zn2+ ions generally held more tightly than structural or regulatory ones. Metal carrier proteins, most of which are not specific for Zn2+, bind these ions with a broad range of affinities that overlap those of catalytic, structural, and regulatory Zn2+ ions and are thought to be responsible for distributing the metal through most cells, tissues, and fluid compartments. While little is known about how many proteins obtain or release these ions, there is now considerable experimental evidence suggesting that metal carrier proteins may be responsible for transferring metals to and from some Zn2+-dependent proteins, thus serving as a major regulatory factor for them. In this review, the biological roles of Zn2+ and structures of Zn2+ binding sites are examined, and experimental evidence demonstrating the direct participation of metal carrier proteins in enzyme regulation is discussed. Mechanisms of metal ion transfer are also offered, and the potential physiological significance of this phenomenon is explored.
Collapse
|
133
|
Burclaff J, Bliton RJ, Breau KA, Ok MT, Gomez-Martinez I, Ranek JS, Bhatt AP, Purvis JE, Woosley JT, Magness ST. A Proximal-to-Distal Survey of Healthy Adult Human Small Intestine and Colon Epithelium by Single-Cell Transcriptomics. Cell Mol Gastroenterol Hepatol 2022; 13:1554-1589. [PMID: 35176508 PMCID: PMC9043569 DOI: 10.1016/j.jcmgh.2022.02.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND & AIMS Single-cell transcriptomics offer unprecedented resolution of tissue function at the cellular level, yet studies analyzing healthy adult human small intestine and colon are sparse. Here, we present single-cell transcriptomics covering the duodenum, jejunum, ileum, and ascending, transverse, and descending colon from 3 human beings. METHODS A total of 12,590 single epithelial cells from 3 independently processed organ donors were evaluated for organ-specific lineage biomarkers, differentially regulated genes, receptors, and drug targets. Analyses focused on intrinsic cell properties and their capacity for response to extrinsic signals along the gut axis across different human beings. RESULTS Cells were assigned to 25 epithelial lineage clusters. Multiple accepted intestinal stem cell markers do not specifically mark all human intestinal stem cells. Lysozyme expression is not unique to human Paneth cells, and Paneth cells lack expression of expected niche factors. Bestrophin 4 (BEST4)+ cells express Neuropeptide Y (NPY) and show maturational differences between the small intestine and colon. Tuft cells possess a broad ability to interact with the innate and adaptive immune systems through previously unreported receptors. Some classes of mucins, hormones, cell junctions, and nutrient absorption genes show unappreciated regional expression differences across lineages. The differential expression of receptors and drug targets across lineages show biological variation and the potential for variegated responses. CONCLUSIONS Our study identifies novel lineage marker genes, covers regional differences, shows important differences between mouse and human gut epithelium, and reveals insight into how the epithelium responds to the environment and drugs. This comprehensive cell atlas of the healthy adult human intestinal epithelium resolves likely functional differences across anatomic regions along the gastrointestinal tract and advances our understanding of human intestinal physiology.
Collapse
Affiliation(s)
- Joseph Burclaff
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - R Jarrett Bliton
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina
| | - Keith A Breau
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Meryem T Ok
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina
| | - Ismael Gomez-Martinez
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jolene S Ranek
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Aadra P Bhatt
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jeremy E Purvis
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - John T Woosley
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Scott T Magness
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill/North Carolina State University, Chapel Hill, North Carolina; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
| |
Collapse
|
134
|
Mapping of MeLiM melanoma combining ICP-MS and MALDI-MSI methods. Int J Biol Macromol 2022; 203:583-592. [PMID: 35090942 DOI: 10.1016/j.ijbiomac.2022.01.139] [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: 10/10/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 11/22/2022]
Abstract
Here we developed a powerful tool for comprehensive data collection and mapping of molecular and elemental signatures in the Melanoma-bearing Libechov Minipig (MeLiM) model. The combination of different mass spectrometric methods allowed for detail investigation of specific melanoma markers and elements and their spatial distribution in tissue sections. MALDI-MSI combined with HPLC-MS/MS analyses resulted in identification of seven specific proteins, S100A12, CD163, MMP-2, galectin-1, tenascin, resistin and PCNA that were presented in the melanoma signatures. Furthermore, the ICP-MS method allowed for spatial detection of zinc, calcium, copper, and iron elements linked with the allocation of the specific binding proteins.
Collapse
|
135
|
Differential Gene Expression Profiles between N-Terminal Domain and Ligand-Binding Domain Inhibitors of Androgen Receptor Reveal Ralaniten Induction of Metallothionein by a Mechanism Dependent on MTF1. Cancers (Basel) 2022; 14:cancers14020386. [PMID: 35053548 PMCID: PMC8773799 DOI: 10.3390/cancers14020386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 02/04/2023] Open
Abstract
Hormonal therapies for prostate cancer target the androgen receptor (AR) ligand-binding domain (LBD). Clinical development for inhibitors that bind to the N-terminal domain (NTD) of AR has yielded ralaniten and its analogues. Ralaniten acetate is well tolerated in patients at 3600 mgs/day. Clinical trials are ongoing with a second-generation analogue of ralaniten. Binding sites on different AR domains could result in differential effects on AR-regulated gene expression. Here, we provide the first comparison between AR-NTD inhibitors and AR-LBD inhibitors on androgen-regulated gene expression in prostate cancer cells using cDNA arrays, GSEA, and RT-PCR. LBD inhibitors and NTD inhibitors largely overlapped in the profile of androgen-induced genes that they each inhibited. However, androgen also represses gene expression by various mechanisms, many of which involve protein-protein interactions. De-repression of the transcriptome of androgen-repressed genes showed profound variance between these two classes of inhibitors. In addition, these studies revealed a unique and strong induction of expression of the metallothionein family of genes by ralaniten by a mechanism independent of AR and dependent on MTF1, thereby suggesting this may be an off-target. Due to the relatively high doses that may be encountered clinically with AR-NTD inhibitors, identification of off-targets may provide insight into potential adverse events, contraindications, or poor efficacy.
Collapse
|
136
|
Hu Y, Fu QY, Fu DN, Wang XL, Wang ZH, Zhang JT, Xu WJ, Zhou GK, Chen LH, Liu T. The Role of Transient Receptor Potential A1 and G Protein-Coupled Receptor 39 in Zinc-Mediated Acute and Chronic Itch in Mice. Front Mol Neurosci 2022; 14:768731. [PMID: 35095413 PMCID: PMC8790520 DOI: 10.3389/fnmol.2021.768731] [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: 09/01/2021] [Accepted: 12/09/2021] [Indexed: 11/24/2022] Open
Abstract
Itching is a common symptom of many skin or systemic diseases and has a negative impact on the quality of life. Zinc, one of the most important trace elements in an organism, plays an important role in the regulation of pain. Whether and how zinc regulates itching is largely unclear. Herein, we explored the role of Zn2+ in the regulation of acute and chronic itch in mice. It is found that intradermal injection (i.d.) of Zn2+ dose-dependently induced acute itch and transient receptor potential A1 (TRPA1) participated in Zn2+-induced acute itch in mice. Moreover, the pharmacological analysis showed the involvement of histamine, mast cells, opioid receptors, and capsaicin-sensitive C-fibers in Zn2+-induced acute itch in mice. Systemic administration of Zn2+ chelators, such as N,N,N′,N′-Tetrakis(2-pyridylmethyl)ethylenediamine (TPEN), pyrithione, and clioquinol were able to attenuate both acute itch and dry skin-induced chronic itch in mice. Quantitative polymerase chain reaction (Q-PCR) analysis showed that the messenger RNA (mRNA) expression levels of zinc transporters (ZIPs and ZnTs) significantly changed in the dorsal root ganglia (DRG) under dry skin-induced chronic itch condition in mice. Activation of extracellular signal-regulated kinase (ERK) pathway was induced in the DRG and skin by the administration of zinc or under dry skin condition, which was inhibited by systemic administration of Zn2+ chelators. Finally, we found that the expression of GPR39 (a zinc-sensing GPCR) was significantly upregulated in the dry skin mice model and involved in the pathogenesis of chronic itch. Together, these results indicated that the TRPA1/GPR39/ERK axis mediated the zinc-induced itch and, thus, targeting zinc signaling may be a promising strategy for anti-itch therapy.
Collapse
Affiliation(s)
- Yue Hu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou, China
| | - Qing-Yue Fu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou, China
| | - Dan-Ni Fu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou, China
| | - Xue-Long Wang
- Department of Thoracic Surgery, Capital Medical University Electric Power Teaching Hospital Beijing, Beijing, China
| | - Zhi-Hong Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou, China
| | - Jiang-Tao Zhang
- Institute of Pain Medicine and Special Environmental Medicine, Nantong University, Nantong, China
| | - Wen-Jing Xu
- Institute of Pain Medicine and Special Environmental Medicine, Nantong University, Nantong, China
| | - Guo-Kun Zhou
- Institute of Pain Medicine and Special Environmental Medicine, Nantong University, Nantong, China
| | - Li-Hua Chen
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong, China
- Li-Hua Chen
| | - Tong Liu
- Institute of Pain Medicine and Special Environmental Medicine, Nantong University, Nantong, China
- College of Life Sciences, Yanan University, Yan'an, China
- Suzhou Key Laboratory of Intelligent Medicine and Equipment, Soochow University, Suzhou, China
- *Correspondence: Tong Liu
| |
Collapse
|
137
|
The Impact of Fullerenes as Doxorubicin Nano-Transporters on Metallothionein and Superoxide Dismutase Status in MCF-10A Cells. Pharmaceutics 2022; 14:pharmaceutics14010102. [PMID: 35056998 PMCID: PMC8777724 DOI: 10.3390/pharmaceutics14010102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 01/27/2023] Open
Abstract
This study aimed to synthesise C60–DOX complexes followed by the analysis of their effect on the concentration of metallothionein (MT) as a non-enzymatic antioxidant and on the concentration and activity of superoxide dismutase (SOD) as an antioxidant enzyme in healthy human mammary MCF-10A cells. Dynamic light scattering and electrophoretic light scattering were used to establish the size and zeta potential of the complexes. The MT and SOD concentrations were determined using the ELISA method; SOD activity was determined by tetrazolium salt reduction inhibition. Lower MT concentration following exposure of cells to both DOX and C60 fullerene compared to the control sample was found. However, the concentration of this protein increased as a consequence of the C60–DOX complexes action on MCF-10A cells compared to the control. C60 used alone did not affect the concentration and activity of SOD in MCF-10A cells. Application of free DOX did not activate cellular antioxidant defence in the form of an increase in SOD concentration or its activity. In contrast treatment of cells with the C60–DOX complex resulted in a decrease in SOD1 concentration and a significant increase in SOD activity compared to cells treated with free DOX, C60 and control. Thus, it was found that C60–DOX complexes showed potential for protective effects against DOX-induced toxicity to MCF-10A cells.
Collapse
|
138
|
Li W, Liu Z, Cen X, Xu J, Zhao S, Wang B, Zhang W, Qiu M. Integrated analysis of fibroblasts molecular features in papillary thyroid cancer combining single-cell and bulk RNA sequencing technology. Front Endocrinol (Lausanne) 2022; 13:1019072. [PMID: 36387901 PMCID: PMC9643292 DOI: 10.3389/fendo.2022.1019072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Papillary thyroid cancer (PTC) is the most common pathological type of thyroid cancer with a high incidence globally. Increasing evidence reported that fibroblasts infiltration in cancer was correlated with prognostic outcomes. However, fibroblasts related study in thyroid cancer remains deficient. METHODS Single-cell sequencing data of PTC were analyzed by Seurat R package to explore the ecosystem in PTC and identify fibroblasts cluster. The expression profiles and prognostic values of fibroblast related genes were assessed in TCGA dataset. A fibrosis score model was established for prognosis prediction in thyroid cancer patients. Differentially expressed genes and functional enrichment between high and low fibrosis score groups in TCGA dataset were screened. The correlation of immune cells infiltration and fibrosis score in thyroid cancer patients was explored. Expression levels and prognostic values of key fibroblast related factor were validated in clinical tissues another PTC cohort. RESULTS Fibroblasts were highly infiltrated in PTC and could interact with other type of cells by single-cell data analysis. 34 fibroblast related terms were differentially expressed in thyroid tumor tissues. COX regression analysis suggested that the constructed fibrosis score model was an independent prognostic predictor for thyroid cancer patients (HR = 5.17, 95%CI 2.31-11.56, P = 6.36E-05). Patients with low fibrosis scores were associated with a significantly better overall survival (OS) than those with high fibrosis scores in TCGA dataset (P = 7.659E-04). Specific immune cells infiltration levels were positively correlated with fibrosis score, including monocytes, M1 macrophages and eosinophils. CONCLUSION Our research demonstrated a comprehensive horizon of fibroblasts features in thyroid cancer microenvironment, which may provide potential value for thyroid cancer treatment.
Collapse
Affiliation(s)
- Wei Li
- Department of General Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Zhiyong Liu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaoxia Cen
- Department of General Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Jing Xu
- Department of General Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Suo Zhao
- Department of General Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Bin Wang
- Department of General Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
| | - Wei Zhang
- Department of General Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
- *Correspondence: Ming Qiu, ; Wei Zhang,
| | - Ming Qiu
- Department of General Surgery, Changzheng Hospital, Navy Medical University, Shanghai, China
- *Correspondence: Ming Qiu, ; Wei Zhang,
| |
Collapse
|
139
|
Huang P, Zhang B, Zhao J, Li MD. Integrating the Epigenome and Transcriptome of Hepatocellular Carcinoma to Identify Systematic Enhancer Aberrations and Establish an Aberrant Enhancer-Related Prognostic Signature. Front Cell Dev Biol 2022; 10:827657. [PMID: 35300417 PMCID: PMC8921559 DOI: 10.3389/fcell.2022.827657] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/31/2022] [Indexed: 12/22/2022] Open
Abstract
Recently, emerging evidence has indicated that aberrant enhancers, especially super-enhancers, play pivotal roles in the transcriptional reprogramming of multiple cancers, including hepatocellular carcinoma (HCC). In this study, we performed integrative analyses of ChIP-seq, RNA-seq, and whole-genome bisulfite sequencing (WGBS) data to identify intergenic differentially expressed enhancers (DEEs) and genic differentially methylated enhancers (DMEs), along with their associated differentially expressed genes (DEE/DME-DEGs), both of which were also identified in independent cohorts and further confirmed by HiC data. Functional enrichment and prognostic model construction were conducted to explore the functions and clinical significance of the identified enhancer aberrations. We identified a total of 2,051 aberrant enhancer-associated DEGs (AE-DEGs), which were highly concurrent in multiple HCC datasets. The enrichment results indicated the significant overrepresentations of crucial biological processes and pathways implicated in cancer among these AE-DEGs. A six AE-DEG-based prognostic signature, whose ability to predict the overall survival of HCC was superior to that of both clinical phenotypes and previously published similar prognostic signatures, was established and validated in TCGA-LIHC and ICGC-LIRI cohorts, respectively. In summary, our integrative analysis depicted a landscape of aberrant enhancers and associated transcriptional dysregulation in HCC and established an aberrant enhancer-derived prognostic signature with excellent predictive accuracy, which might be beneficial for the future development of epigenetic therapy for HCC.
Collapse
Affiliation(s)
- Peng Huang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bin Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Junsheng Zhao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ming D. Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Research Center for Air Pollution and Health, Zhejiang University, Hangzhou, China
- *Correspondence: Ming D. Li,
| |
Collapse
|
140
|
Distinct Hypoxia-Related Gene Profiling Characterizes Clinicopathological Features and Immune Status of Mismatch Repair-Deficient Colon Cancer. JOURNAL OF ONCOLOGY 2021; 2021:2427427. [PMID: 34917146 PMCID: PMC8670907 DOI: 10.1155/2021/2427427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/07/2021] [Accepted: 11/13/2021] [Indexed: 12/09/2022]
Abstract
Despite dramatic responses to immune checkpoint inhibitors (ICIs) in patients with colon cancer (CC) harboring deficient mismatch repair (dMMR), more than half of these patients ultimately progress and experience primary or secondary drug resistance. There is no useful biomarker that is currently validated to accurately predict this resistance or stratify patients who may benefit from ICI-based immunotherapy. As hypoxic and acidic tumor microenvironment would greatly impair tumor-suppressing functions of tumor-infiltrating lymphocytes (TILs), we sought to explore distinct immunological phenotypes by analysis of the intratumoral hypoxia state using a well-established gene signature. Based on the Gene Expression Omnibus (GEO) (n = 88) and The Cancer Genome Atlas (TCGA) (n = 49) databases of patients with CC, we found that dMMR CC patients could be separated into normoxia subgroup (NS) and hypoxia subgroup (HS) with different levels of expression of hypoxia-related genes (lower in NS group and higher in HS group) using NMF package. Tumoral parenchyma in the HS group had a relatively lower level of immune cell infiltration, particularly CD8+ T cells and M1 macrophages than the NS group, and coincided with higher expression of immune checkpoint molecules and C-X-C motif chemokines, which might be associated with ICI resistance and prognosis. Furthermore, three genes, namely, MT1E, MT2A, and MAFF, were identified to be differentially expressed between NS and HS groups in both GEO and TCGA cohorts. Based on these genes, a prognostic model with stable and valuable predicting ability has been built for clinical application. In conclusion, the varying tumor-immune microenvironment (TIME) classified by hypoxia-related genes might be closely associated with different therapeutic responses of ICIs and prognosis of dMMR CC patients.
Collapse
|
141
|
Abstract
The functions, purposes, and roles of metallothioneins have been the subject of speculations since the discovery of the protein over 60 years ago. This article guides through the history of investigations and resolves multiple contentions by providing new interpretations of the structure-stability-function relationship. It challenges the dogma that the biologically relevant structure of the mammalian proteins is only the one determined by X-ray diffraction and NMR spectroscopy. The terms metallothionein and thionein are ambiguous and insufficient to understand biological function. The proteins need to be seen in their biological context, which limits and defines the chemistry possible. They exist in multiple forms with different degrees of metalation and types of metal ions. The homoleptic thiolate coordination of mammalian metallothioneins is important for their molecular mechanism. It endows the proteins with redox activity and a specific pH dependence of their metal affinities. The proteins, therefore, also exist in different redox states of the sulfur donor ligands. Their coordination dynamics allows a vast conformational landscape for interactions with other proteins and ligands. Many fundamental signal transduction pathways regulate the expression of the dozen of human metallothionein genes. Recent advances in understanding the control of cellular zinc and copper homeostasis are the foundation for suggesting that mammalian metallothioneins provide a highly dynamic, regulated, and uniquely biological metal buffer to control the availability, fluctuations, and signaling transients of the most competitive Zn(II) and Cu(I) ions in cellular space and time.
Collapse
Affiliation(s)
- Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław 50-383, Poland
| | - Wolfgang Maret
- Departments of Biochemistry and Nutritional Sciences, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London SE1 9NH, U.K
| |
Collapse
|
142
|
Tarabay HH, Abol-Enein H, Awadalla A, Mortada WI, Abdel-Aziz AF. Gene expression and oxidative stress markers profile associated with toxic metals in patients with renal cell carcinoma. Mol Biol Rep 2021; 49:1161-1169. [PMID: 34851477 DOI: 10.1007/s11033-021-06944-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 11/08/2021] [Indexed: 01/12/2023]
Abstract
BACKGROUND Toxic metals are associated with cancer progression. Studies have reported the relation between some toxic metals and renal cell carcinoma (RCC). METHODS AND RESULTS Blood levels of Cd and Pb were determined in 94 RCC patients (RCC group) and 91 matched controls as well as blood level of malondialdehyde (MDA) and catalase (CAT) activity as markers of oxidative stress and antioxidant, respectively. Gene expression of MAP kinase pathway (P38 and JNK), hypoxia-inducible factor 1-alpha (HIF1α), vascular endothelial growth factor (VEGF), cytochrome C oxidase subunit 6 (COX6), metallothionein (MT2A), and heat shock protein (HSP90AA1) were evaluated in the obtained tissue specimens. Blood Cd and Pb levels were significantly higher in RCC group comparing to control group with preferential significant increase of Cd in chromophobe RCC (chRCC) sub-type. MDA level was significantly higher and CAT activity was lower in the RCC compared to controls. The difference was evident only in chRCC. The expressions of genes were significantly increased in the cancer tissues than in non-cancerous tissues in RCC sub-types and there was a significant correlation between Cd levels and expression of genes VEGF, MT2A, P38 and JNK in chRCC group. Immunohistochemical staining of clear cell RCC tissues shows a marked expression of VEGF and HIF-1α.While COX6 staining show marked expression in chRCC. CONCLUSIONS There is a positive correlation between Cd toxicity and the development of RCC, especially chRCC sub-type. Cd is strongly incriminated in the pathogenesis of chRCC through the effort on some genes and oxidative stress markers.
Collapse
Affiliation(s)
- Heba H Tarabay
- Department of Chemistry, Biochemistry Division, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Hassan Abol-Enein
- Center of Excellence for Genome and Cancer Research, Urology and Nephrology Center, Mansoura University, PO: 135516, Mansoura, 35516, Egypt.
| | - Amira Awadalla
- Center of Excellence for Genome and Cancer Research, Urology and Nephrology Center, Mansoura University, PO: 135516, Mansoura, 35516, Egypt
| | - Wael I Mortada
- Clinical Chemistry Laboratory, Urology and Nephrology Center, Mansoura University, Mansoura, 35516, Egypt
| | - A F Abdel-Aziz
- Department of Chemistry, Biochemistry Division, Faculty of Science, Mansoura University, Mansoura, Egypt
| |
Collapse
|
143
|
Sands B, Yun S, Mendenhall AR. Introns control stochastic allele expression bias. Nat Commun 2021; 12:6527. [PMID: 34764277 PMCID: PMC8585970 DOI: 10.1038/s41467-021-26798-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 10/19/2021] [Indexed: 01/26/2023] Open
Abstract
Monoallelic expression (MAE) or extreme allele bias can account for incomplete penetrance, missing heritability and non-Mendelian diseases. In cancer, MAE is associated with shorter patient survival times and higher tumor grade. Prior studies showed that stochastic MAE is caused by stochastic epigenetic silencing, in a gene and tissue-specific manner. Here, we used C. elegans to study stochastic MAE in vivo. We found allele bias/MAE to be widespread within C. elegans tissues, presenting as a continuum from fully biallelic to MAE. We discovered that the presence of introns within alleles robustly decreases MAE. We determined that introns control MAE at distinct loci, in distinct cell types, with distinct promoters, and within distinct coding sequences, using a 5'-intron position-dependent mechanism. Bioinformatic analysis showed human intronless genes are significantly enriched for MAE. Our experimental evidence demonstrates a role for introns in regulating MAE, possibly explaining why some mutations within introns result in disease.
Collapse
Affiliation(s)
- Bryan Sands
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA USA
| | - Soo Yun
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA USA
| | - Alexander R. Mendenhall
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA USA
| |
Collapse
|
144
|
Zhu Y, Sui B, Liu X, Sun J. The reversal of drug resistance by two-dimensional titanium carbide Ti 2 C (2D Ti2C) in non-small-cell lung cancer via the depletion of intracellular antioxidant reserves. Thorac Cancer 2021; 12:3340-3355. [PMID: 34741403 PMCID: PMC8671908 DOI: 10.1111/1759-7714.14208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/09/2021] [Accepted: 10/11/2021] [Indexed: 12/22/2022] Open
Abstract
Background Chemoresistance is a major barrier limiting the therapeutic efficacy of late stage non‐small cell lung cancer (NSCLC). In this study, we sought to use two‐dimensional titanium carbide (2D Ti2C) to reverse cisplatin resistance in NSCLC. Methods We first achieved favorable properties as a potential anti‐tumor agent. We then compared cell viability and cisplatin uptake in chemoresistant NSCLC cells before and after the use of 2D Ti2C. Afterwards, we explored the effects of 2D Ti2C on intracellular antioxidant reserves, followed by evaluating the subsequent changes in the expression of core drug resistance genes. Finally, we confirmed the tumor inhibitory effect and bio‐safety of 2D Ti2C in a drug‐resistant lung cancer model in nude mice. Results Due to the properties of thin layer, large specific surface area, and abundant reactive groups on the surface, 2D Ti2C can deplete the antioxidant reserve systems such as the glutathione redox buffer system, γ‐glutamylcysteine synthetase (γ‐GCS), glutathione peroxidase (GPx), glutathione‐S‐transferase‐Pi (GST‐π), and metallothionein (MT), thereby increasing the intracellular accumulation of cisplatin and decreasing the expression of drug resistance genes. Conclusions 2D Ti2C can reverse NSCLC chemoresistance both in vitro and in vivo, suggesting that it may potentially become a novel and effective means to treat chemoresistant NSCLC in the clinic.
Collapse
Affiliation(s)
- Yue Zhu
- Department of Dental Materials, Shanghai Biomaterials Research & Testing Center, Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Clinical Research Center of Stomatology, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Baiyan Sui
- Department of Dental Materials, Shanghai Biomaterials Research & Testing Center, Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Clinical Research Center of Stomatology, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Xin Liu
- Department of Dental Materials, Shanghai Biomaterials Research & Testing Center, Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Clinical Research Center of Stomatology, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Jiao Sun
- Department of Dental Materials, Shanghai Biomaterials Research & Testing Center, Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Clinical Research Center of Stomatology, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| |
Collapse
|
145
|
Using Genomic and Transcriptome Analyses to Identify the Role of the Oxidative Stress Pathway in Renal Clear Cell Carcinoma and Its Potential Therapeutic Significance. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:5561124. [PMID: 34721758 PMCID: PMC8550864 DOI: 10.1155/2021/5561124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 07/31/2021] [Accepted: 09/08/2021] [Indexed: 12/31/2022]
Abstract
Oxidative stress (OS) refers to endogenous and/or exogenous stimulation when the balance between oxidation and antioxidants in the body is disrupted, resulting in excessive production of free radicals. Excessive free radicals exert a series of negative effects on the body, which can result in the oxidation of and infliction of damage on biological molecules and further cause cell death and tissue damage, which are related to many pathological processes. Pathways related to OS have always been the focus of medical research. Several studies are being conducted to develop strategies to treat cancer by exploring the OS pathways. Therefore, this study is aimed at determining the correlation between the OS pathway and kidney renal clear cell carcinoma (KIRC) through bioinformatics analysis, at proving the effect of common anticancer drugs on the OS pathway, and at constructing a prognosis model of patients with KIRC based on several genes with the strongest correlation between the OS pathway and KIRC. We first collected and analyzed gene expression and clinical information of related patients through TCGA database. Then, we divided the samples into three clusters according to their gene expression levels obtained through cluster analysis. Using these three clusters, we performed GDSC drug analysis and GSEA analysis and examined the correlation among the OS pathway, histone modification, and immune cell infiltration. We also analyzed the response of anti-PD-1 and anti-CTLA-4 to the OS pathway. Thereafter, we used LASSO regression to select the most suitable nine genes, combined with the clinicopathological characteristics to establish the prognosis model of patients with KIRC, and verified the scientific precision of the model. Finally, tumor mutational burden was calculated to verify whether patients would benefit from immunotherapy. The results of this study may provide a reference for the establishment of treatment strategies for patients with KIRC.
Collapse
|
146
|
Lichołai S, Studzińska D, Plutecka H, Gubała T, Szczeklik W, Sanak M. MiR-191 as a Key Molecule in Aneurysmal Aortic Remodeling. Biomolecules 2021; 11:1611. [PMID: 34827608 PMCID: PMC8615628 DOI: 10.3390/biom11111611] [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] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 12/03/2022] Open
Abstract
Abdominal aortic aneurysms (AAA) are a complex disease with an unclear pathomechanism. A positive family history is emphasized as a significant risk factor, and a nonspecific model of inheritance suggests participation of epigenetic regulation in the pathogenesis of this disease. Past studies have implicated microRNAs in the development of AAA; therefore in this project, we measured miR-191 levels in AAA patients and compared them with a control group. We found that miR-191 levels were significantly elevated in aneurysmal patients, although this did not correlate with the available clinical data. We then developed an in vitro model where, using cells with an endothelial phenotype, we determined the effect of miR-191 on the transcriptome using RNA sequencing. Subsequent pathway analysis established that some of the perturbations mediated by miR-191 can be explained by several processes which have long been observed and described in literature as accompanying the development of abdominal aortic aneurysms.
Collapse
Affiliation(s)
- Sabina Lichołai
- Division of Molecular Biology and Clinical Genetics, Faculty of Medicine, Jagiellonian University Medical College, Skawinska 8, 31-066 Kraków, Poland; (H.P.); (M.S.)
| | - Dorota Studzińska
- Department of Intensive Care and Perioperative Medicine, Faculty of Medicine, Jagiellonian University Medical College, Wrocławska 1/3, 30-901 Kraków, Poland; (D.S.); (W.S.)
| | - Hanna Plutecka
- Division of Molecular Biology and Clinical Genetics, Faculty of Medicine, Jagiellonian University Medical College, Skawinska 8, 31-066 Kraków, Poland; (H.P.); (M.S.)
| | - Tomasz Gubała
- Sano Centre for Computational Medicine, Czarnowiejska 36, 30-054 Kraków, Poland;
| | - Wojciech Szczeklik
- Department of Intensive Care and Perioperative Medicine, Faculty of Medicine, Jagiellonian University Medical College, Wrocławska 1/3, 30-901 Kraków, Poland; (D.S.); (W.S.)
| | - Marek Sanak
- Division of Molecular Biology and Clinical Genetics, Faculty of Medicine, Jagiellonian University Medical College, Skawinska 8, 31-066 Kraków, Poland; (H.P.); (M.S.)
| |
Collapse
|
147
|
Kusakabe M, Sato M, Nakamura Y, Mikami H, Lin J, Nagase H. Elemental analysis by Metallobalance provides a complementary support layer over existing blood biochemistry panel-based cancer risk assessment. PeerJ 2021; 9:e12247. [PMID: 34707935 PMCID: PMC8496461 DOI: 10.7717/peerj.12247] [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: 07/01/2021] [Accepted: 09/13/2021] [Indexed: 11/20/2022] Open
Abstract
Despite the benefit of early cancer screening, Japan has one of the lowest cancer screening rates among developed countries, possibly due to there being a lack of “a good test” that can provide sufficient levels of test sensitivity and accuracy without a large price tag. As a number of essential and trace elements have been intimately connected to the oncogenesis of cancer, Metallobalance, a recent development in elemental analysis utilizing the technique of inductively coupled plasma mass spectrometry has been developed and tested as a robust method for arrayed cancer risk screening. We have conducted case-control epidemiological studies in the prefecture of Chiba, in the Greater Tokyo Area, and sought to determine both Metallobalance screening’s effectiveness for predicting pan-cancer outcomes, and whether the method is capable enough to replace the more conventional antigen-based testing methods. Results suggest that MB screening provides some means of classification potential among cancer and non-cancer cases, and may work well as a complementary method to traditional antigen-based tumor marker testing, even in situations where tumor markers alone cannot discernibly identify cancer from non-cancer cases.
Collapse
Affiliation(s)
- Miho Kusakabe
- Graduate School of Medical and Pharmaceutical Sciences, Chiba University, Chiba, Japan.,Cancer Prevention Center, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Masahiro Sato
- Cancer Prevention Center, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Yohko Nakamura
- Cancer Prevention Center, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Haruo Mikami
- Cancer Prevention Center, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Jason Lin
- Division of Clinical Genomics, Chiba Cancer Center Research Institute, Chiba, Japan.,Division of Cancer Genetics, Chiba Cancer Center Research Institute, Chiba, Japan
| | - Hiroki Nagase
- Graduate School of Medical and Pharmaceutical Sciences, Chiba University, Chiba, Japan.,Division of Cancer Genetics, Chiba Cancer Center Research Institute, Chiba, Japan
| |
Collapse
|
148
|
Phillips-Chavez C, Coward J, Watson M, Schloss J. A Retrospective Cross-Sectional Cohort Trial Assessing the Prevalence of MTHFR Polymorphisms and the Influence of Diet on Platinum Resistance in Ovarian Cancer Patients. Cancers (Basel) 2021; 13:5215. [PMID: 34680361 PMCID: PMC8533864 DOI: 10.3390/cancers13205215] [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: 09/22/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 11/29/2022] Open
Abstract
Ovarian cancer has the lowest survival rate in gynaecologic malignancies with a 5-year survival rate of 43%. Platinum resistance is one of the main drivers of ovarian cancer mortality, of which aberrant methylation has been cited as a significant contributor. Understanding the essential role of the methylenetetrahydrofolate reductase enzyme (MTHFR) on DNA synthesis and repair, and how nutrient status can vastly affect its performance, led to the investigation of MTHFR status and dietary influence on platinum response in epithelial ovarian cancer (EOC) patients. Twenty-five adult female patients who completed first-line platinum-based chemotherapy for primary ovarian cancer were selected from Icon Cancer Centres in Australia. Participants were grouped based on platinum response. A full medical and family history, food frequency questionnaire and single blood test were completed, testing for MTHFR polymorphisms, serum folate, serum and active B12 and homocysteine levels. Nineteen of twenty-five participants had an MTHFR polymorphism. Of those, 20% were compound heterozygous, 12% were heterozygous C677T (CT), 4% homozygous C677T, 12% homozygous A1298C and 28% were heterozygous A1298C (AC). Statistically significant associations were found between dietary zinc (p = 0.0086; 0.0030; 0.0189) and B12 intakes in CT genotypes (p = 0.0157; 0.0030; 0.0068) indicating that zinc or vitamin B12 intakes below RDI were associated with this genotype. There were strong associations of vitamin B6 intakes in AC genotypes (p = 0.0597; 0.0547; 0.0610), and dietary folate in compound heterozygotes with sensitive and partially sensitive disease (p = 0.0627; 0.0510). There were also significant associations between serum folate (p = 0.0478) and dietary B12 (p = 0.0350) intakes above RDI and platinum sensitivity in wild-types as well as strong associations with homocysteine levels (p = 0.0886) and zinc intake (p = 0.0514). Associations with dietary B12 (p = 0.0514) and zinc intakes (p = 0.0731) were also strong in resistant wild types. Results indicate that dietary zinc, B12 and B6 intakes may be associated with platinum sensitivity dependent on MTHFR genotype. These results require further research to clarify the dosages necessary to elicit a response; however, they provide a novel foundation for acknowledging the role of diet on treatment response in EOC.
Collapse
Affiliation(s)
- Caitlin Phillips-Chavez
- Icon Cancer Centre, Queensland, Australia;
- Endeavour College of Natural Health, Brisbane, QLD 4006, Australia;
| | - Jermaine Coward
- Icon Cancer Centre, Queensland, Australia;
- School of Medicine, University of Queensland, Brisbane, QLD 4006, Australia
| | - Michael Watson
- Endeavour College of Natural Health, Brisbane, QLD 4006, Australia;
- Institute of Health & Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4006, Australia
| | - Janet Schloss
- NCNM, Southern Cross University, Lismore, NSW 2480, Australia;
| |
Collapse
|
149
|
Liu Z, Ma H, Lai Z. Revealing the potential mechanism of Astragalus membranaceus improving prognosis of hepatocellular carcinoma by combining transcriptomics and network pharmacology. BMC Complement Med Ther 2021; 21:263. [PMID: 34663301 PMCID: PMC8522094 DOI: 10.1186/s12906-021-03425-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the fourth leading cause of cancer-related death. Traditional Chinese medicine (TCM) has special advantages in relieving HCC, while Astragalus membranaceus is commonly used in TCM treatment. However, its underlying mechanisms for treatment of HCC are unclear. Methods Differentially expressed genes (DEGs) of Astragalus membranaceus treatment in HepG2 cells were identified, and Astragalus membranaceus-gene network was constructed. The hub genes were then obtained via protein-protein interaction (PPI) analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and Gene Set Enrichment Analysis (GSEA) were subsequently performed. Furthermore, prognosis genes related to HCC from The Cancer Genome Atlas Program (TCGA) was identified to explore the correlation between Astragalus membranaceus treatment and prognosis of HCC. Finally, Astragalus membranaceus-component-target network was established through SymMap. Results Twenty five DEGs (15 up-regulated and 10 down-regulated) of Astragalus membranaceus treatment in HepG2 cells were identified. Among the 25 genes, MT1F, MT1G, MT1X and HMOX1 may play essential roles. Astragalus membranaceus mainly affects the Mineral absorption pathway in HCC. A total of 256 genes (p < 0.01) related to prognosis of HCC were identified, and MT1G is a common gene between prognosis genes and DEGs. Furthermore, Astragalus membranaceus may directly down-regulate MT1G through daidzein to promote ferroptosis of HCC cells and improve prognosis for HCC. Conclusion Our study provided new understandings of the pharmacological mechanisms by which Astragalus membranaceus improves the prognosis of HCC, and showed that the combination of transcriptomics and network pharmacology is helpful to explore mechanisms of TCM and traditional medicines from other nations. Supplementary Information The online version contains supplementary material available at 10.1186/s12906-021-03425-9.
Collapse
Affiliation(s)
- Zhili Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China. .,Key Laboratory of Brain Functional Genomics (East China Normal University), Ministry of Education, School of Life Sciences, East China Normal University, Shanghai, 200062, China.
| | - Huihan Ma
- Department of Neurology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China.,Department of Neurology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510120, China
| | - Zelin Lai
- Key Laboratory of Brain Functional Genomics (East China Normal University), Ministry of Education, School of Life Sciences, East China Normal University, Shanghai, 200062, China.
| |
Collapse
|
150
|
Buchtova T, Skrott Z, Chroma K, Rehulka J, Dzubak P, Hajduch M, Lukac D, Arampatzis S, Bartek J, Mistrik M. Cannabidiol-induced activation of the metallothionein pathway impedes anticancer effects of disulfiram and its metabolite CuET. Mol Oncol 2021; 16:1541-1554. [PMID: 34632694 PMCID: PMC8978514 DOI: 10.1002/1878-0261.13114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/21/2021] [Accepted: 10/08/2021] [Indexed: 12/29/2022] Open
Abstract
Disulfiram (DSF), an established alcohol‐aversion drug, is a candidate for repurposing in cancer treatment. DSF’s antitumor activity is supported by preclinical studies, case reports, and small clinical trials; however, ongoing clinical trials of advanced‐stage cancer patients encounter variable results. Here, we show that one reason for the inconsistent clinical effects of DSF may reflect interference by other drugs. Using a high‐throughput screening and automated microscopy, we identify cannabidiol, an abundant component of the marijuana plant used by cancer patients to mitigate side effects of chemotherapy, as a likely cause of resistance to DSF. Mechanistically, in cancer cells, cannabidiol triggers the expression of metallothioneins providing protective effects by binding heavy metal‐based substances including the bis‐diethyldithiocarbamate‐copper complex (CuET). CuET is the documented anticancer metabolite of DSF, and we show here that the CuET’s anticancer toxicity is effectively neutralized by metallothioneins. Overall, this work highlights an example of undesirable interference between cancer therapy and the concomitant usage of marijuana products. In contrast, we report that insufficiency of metallothioneins sensitizes cancer cells toward CuET, suggesting a potential predictive biomarker for DSF repurposing in oncology.
Collapse
Affiliation(s)
- Tereza Buchtova
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic
| | - Zdenek Skrott
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic
| | - Katarina Chroma
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic
| | - Jiri Rehulka
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic
| | - Petr Dzubak
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic
| | - Marian Hajduch
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic
| | - David Lukac
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic
| | | | - Jiri Bartek
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic.,Danish Cancer Society Research Center, Copenhagen, Denmark.,Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Martin Mistrik
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacky University, Olomouc, Czech Republic
| |
Collapse
|