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Liu H, Shi K, Wei Z, Zhang Y, Li J. T cell-mediated tumor killing based signature to predict the prognosis and immunotherapy for glioblastoma. Heliyon 2024; 10:e31207. [PMID: 38813229 PMCID: PMC11133811 DOI: 10.1016/j.heliyon.2024.e31207] [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: 08/08/2023] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024] Open
Abstract
Despite the significant advancements in cancer treatment brought by immune checkpoint inhibitors (ICIs), their effectiveness in treating glioblastoma (GBM) remains highly dissatisfactory. Immunotherapy relies on the fundamental concept of T cell-mediated tumor killing (TTK). Nevertheless, additional investigation is required to explore its potential in prognostic prediction and regulation of tumor microenvironment (TME) in GBM. TTK sensitivity related genes (referred to as GSTTKs) were obtained from the TISIDB. The training cohort was available from the TCGA-GBM, while the independent validation group was gathered from GEO database. Firstly, we examined differentially expressed GSTTKs (DEGs) with limma package. Afterwards, the prognostic DEGs were identified and the TTK signature was established with univariate and LASSO Cox analyses. Next, we examined the correlation between the TTK signature and outcome of GBM as well as immune phenotypes of TME. Furthermore, the evaluation of TTK signature in predicting the effectiveness of immunotherapy has also been conducted. We successfully developed a TTK signature with an independent predictive value. Patients who had a high score experienced a worse prognosis compared to patients with low scores. The TTK signature showed a strong positive association with the infiltration degree of immunocyte and the presence of various immune checkpoints. Moreover, individuals with a lower score exhibited increased responsiveness to ICIs and experienced improved prognosis. In conclusions, we successfully developed and verified a TTK signature that has the ability to predict the outcome and immune characteristics of GBM. Furthermore, the TTK signature has the potential to direct the personalized immunotherapy for GBM.
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Affiliation(s)
- Hongchao Liu
- Department of Pathology, The Yiluo Hospital of Luoyang, The Teaching Hospital of Henan University of Science and Technology, Luoyang, China
| | - Kangke Shi
- Department of Pathology, The Yiluo Hospital of Luoyang, The Teaching Hospital of Henan University of Science and Technology, Luoyang, China
| | - Zhihao Wei
- Department of Pathology, The Yiluo Hospital of Luoyang, The Teaching Hospital of Henan University of Science and Technology, Luoyang, China
| | - Yu Zhang
- Department of Pathology, The Yiluo Hospital of Luoyang, The Teaching Hospital of Henan University of Science and Technology, Luoyang, China
| | - Jiaqiong Li
- Department of Pathology, The Yiluo Hospital of Luoyang, The Teaching Hospital of Henan University of Science and Technology, Luoyang, China
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2
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Eralp B, Sefer E. Reference-free inferring of transcriptomic events in cancer cells on single-cell data. BMC Cancer 2024; 24:607. [PMID: 38769480 PMCID: PMC11107047 DOI: 10.1186/s12885-024-12331-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/02/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Cancerous cells' identity is determined via a mixture of multiple factors such as genomic variations, epigenetics, and the regulatory variations that are involved in transcription. The differences in transcriptome expression as well as abnormal structures in peptides determine phenotypical differences. Thus, bulk RNA-seq and more recent single-cell RNA-seq data (scRNA-seq) are important to identify pathogenic differences. In this case, we rely on k-mer decomposition of sequences to identify pathogenic variations in detail which does not need a reference, so it outperforms more traditional Next-Generation Sequencing (NGS) analysis techniques depending on the alignment of the sequences to a reference. RESULTS Via our alignment-free analysis, over esophageal and glioblastoma cancer patients, high-frequency variations over multiple different locations (repeats, intergenic regions, exons, introns) as well as multiple different forms (fusion, polyadenylation, splicing, etc.) could be discovered. Additionally, we have analyzed the importance of less-focused events systematically in a classic transcriptome analysis pipeline where these events are considered as indicators for tumor prognosis, tumor prediction, tumor neoantigen inference, as well as their connection with respect to the immune microenvironment. CONCLUSIONS Our results suggest that esophageal cancer (ESCA) and glioblastoma processes can be explained via pathogenic microbial RNA, repeated sequences, novel splicing variants, and long intergenic non-coding RNAs (lincRNAs). We expect our application of reference-free process and analysis to be helpful in tumor and normal samples differential scRNA-seq analysis, which in turn offers a more comprehensive scheme for major cancer-associated events.
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Affiliation(s)
- Batuhan Eralp
- Department of Computer Science, Ozyegin University, Istanbul, Turkey
| | - Emre Sefer
- Department of Computer Science, Ozyegin University, Istanbul, Turkey.
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3
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Xu C, Hou P, Li X, Xiao M, Zhang Z, Li Z, Xu J, Liu G, Tan Y, Fang C. Comprehensive understanding of glioblastoma molecular phenotypes: classification, characteristics, and transition. Cancer Biol Med 2024; 21:j.issn.2095-3941.2023.0510. [PMID: 38712813 PMCID: PMC11131044 DOI: 10.20892/j.issn.2095-3941.2023.0510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/28/2024] [Indexed: 05/08/2024] Open
Abstract
Among central nervous system-associated malignancies, glioblastoma (GBM) is the most common and has the highest mortality rate. The high heterogeneity of GBM cell types and the complex tumor microenvironment frequently lead to tumor recurrence and sudden relapse in patients treated with temozolomide. In precision medicine, research on GBM treatment is increasingly focusing on molecular subtyping to precisely characterize the cellular and molecular heterogeneity, as well as the refractory nature of GBM toward therapy. Deep understanding of the different molecular expression patterns of GBM subtypes is critical. Researchers have recently proposed tetra fractional or tripartite methods for detecting GBM molecular subtypes. The various molecular subtypes of GBM show significant differences in gene expression patterns and biological behaviors. These subtypes also exhibit high plasticity in their regulatory pathways, oncogene expression, tumor microenvironment alterations, and differential responses to standard therapy. Herein, we summarize the current molecular typing scheme of GBM and the major molecular/genetic characteristics of each subtype. Furthermore, we review the mesenchymal transition mechanisms of GBM under various regulators.
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Affiliation(s)
- Can Xu
- School of Clinical Medicine, Hebei University, Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding 07100, China
- Hebei Key Laboratory of Precise Diagnosis and Treatment of Glioma, Baoding 071000, China
| | - Pengyu Hou
- Hebei Key Laboratory of Precise Diagnosis and Treatment of Glioma, Baoding 071000, China
- School of Basic Medical Sciences, Hebei University, Baoding 07100, China
| | - Xiang Li
- School of Basic Medical Sciences, Hebei University, Baoding 07100, China
| | - Menglin Xiao
- School of Clinical Medicine, Hebei University, Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding 07100, China
- Hebei Key Laboratory of Precise Diagnosis and Treatment of Glioma, Baoding 071000, China
| | - Ziqi Zhang
- School of Clinical Medicine, Hebei University, Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding 07100, China
- Hebei Key Laboratory of Precise Diagnosis and Treatment of Glioma, Baoding 071000, China
| | - Ziru Li
- Hebei Key Laboratory of Precise Diagnosis and Treatment of Glioma, Baoding 071000, China
- School of Basic Medical Sciences, Hebei University, Baoding 07100, China
| | - Jianglong Xu
- School of Clinical Medicine, Hebei University, Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding 07100, China
- Hebei Key Laboratory of Precise Diagnosis and Treatment of Glioma, Baoding 071000, China
| | - Guoming Liu
- School of Clinical Medicine, Hebei University, Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding 07100, China
- Hebei Key Laboratory of Precise Diagnosis and Treatment of Glioma, Baoding 071000, China
| | - Yanli Tan
- Hebei Key Laboratory of Precise Diagnosis and Treatment of Glioma, Baoding 071000, China
- School of Basic Medical Sciences, Hebei University, Baoding 07100, China
- Department of Pathology, Affiliated Hospital of Hebei University, Baoding 07100, China
| | - Chuan Fang
- School of Clinical Medicine, Hebei University, Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding 07100, China
- Hebei Key Laboratory of Precise Diagnosis and Treatment of Glioma, Baoding 071000, China
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4
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Turkowski K, Herzberg F, Günther S, Weigert A, Haselbauer T, Fink L, Brunn D, Grimminger F, Seeger W, Sültmann H, Stiewe T, Pullamsetti SS, Savai R. miR-147b mediated suppression of DUSP8 promotes lung cancer progression. Oncogene 2024; 43:1178-1189. [PMID: 38396293 PMCID: PMC11014796 DOI: 10.1038/s41388-024-02969-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024]
Abstract
Dual-specificity phosphatase 8 (DUSP8) plays an important role as a selective c-Jun N-terminal kinase (JNK) phosphatase in mitogen-activated protein kinase (MAPK) signaling. In this study, we found that DUSP8 is silenced by miR-147b in patients with lung adenocarcinoma (LUAD), which correlates with poor overall survival. Overexpression of DUSP8 resulted in a tumor-suppressive phenotype in vitro and in vivo experimental models, whereas silencing DUSP8 with a siRNA approach abrogated the tumor-suppressive properties. We found that miR-147b is a posttranscriptional regulator of DUSP8 that is highly expressed in patients with LUAD and is associated with lower survival. NanoString analysis revealed that the MAPK signaling pathway is mainly affected by overexpression of miR-147b, leading to increased proliferation and migration and decreased apoptosis in vitro. Moreover, induction of miR-147b promotes tumor progression in vitro and in vivo experimental models. Knockdown of miR-147b restored DUSP8, decreased tumor progression in vitro, and increased apoptosis via JNK phosphorylation. These results suggest that miR-147b plays a key role in regulating MAPK signaling in LUAD. The link between DUSP8 and miR-147b may provide novel approaches for the treatment of lung cancer.
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Affiliation(s)
- Kati Turkowski
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), Bad Nauheim, 61231, Germany
- Institute for Lung Health (ILH), Justus Liebig University, 35392, Giessen, Germany
| | - Frederik Herzberg
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), Bad Nauheim, 61231, Germany
| | - Stefan Günther
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), Bad Nauheim, 61231, Germany
| | - Andreas Weigert
- Goethe-University Frankfurt, Faculty of Medicine, Institute of Biochemistry I, Frankfurt, Germany
- Frankfurt Cancer Institute (FCI), Goethe University, and German Cancer Consortium (DKTK), Hesse, Germany
| | - Tamara Haselbauer
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), Bad Nauheim, 61231, Germany
| | - Ludger Fink
- Institute of Pathology and Cytology, UEGP, Wetzlar, Germany
| | - David Brunn
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), Bad Nauheim, 61231, Germany
| | - Friedrich Grimminger
- Institute for Lung Health (ILH), Justus Liebig University, 35392, Giessen, Germany
- Department of Internal Medicine, Member of the DZL, Member of CPI, Justus Liebig University, 35392, Giessen, Germany
| | - Werner Seeger
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), Bad Nauheim, 61231, Germany
- Institute for Lung Health (ILH), Justus Liebig University, 35392, Giessen, Germany
- Department of Internal Medicine, Member of the DZL, Member of CPI, Justus Liebig University, 35392, Giessen, Germany
| | - Holger Sültmann
- Cancer Genome Research Group, German Cancer Research Center (DKFZ), Germany Center for Lung Research (DZL), and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Thorsten Stiewe
- Institute for Lung Health (ILH), Justus Liebig University, 35392, Giessen, Germany
- Institute of Molecular Oncology, Philipps-University, 35043, Marburg, Germany
| | - Soni S Pullamsetti
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), Bad Nauheim, 61231, Germany
- Institute for Lung Health (ILH), Justus Liebig University, 35392, Giessen, Germany
- Department of Internal Medicine, Member of the DZL, Member of CPI, Justus Liebig University, 35392, Giessen, Germany
| | - Rajkumar Savai
- Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Member of the Cardio-Pulmonary Institute (CPI), Bad Nauheim, 61231, Germany.
- Institute for Lung Health (ILH), Justus Liebig University, 35392, Giessen, Germany.
- Frankfurt Cancer Institute (FCI), Goethe University, and German Cancer Consortium (DKTK), Hesse, Germany.
- Department of Internal Medicine, Member of the DZL, Member of CPI, Justus Liebig University, 35392, Giessen, Germany.
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5
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Stavely R, Hotta R, Guyer RA, Picard N, Rahman AA, Omer M, Soos A, Szocs E, Mueller J, Goldstein AM, Nagy N. A distinct transcriptome characterizes neural crest-derived cells at the migratory wavefront during enteric nervous system development. Development 2023; 150:dev201090. [PMID: 36779913 PMCID: PMC10108706 DOI: 10.1242/dev.201090] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 02/03/2023] [Indexed: 02/14/2023]
Abstract
Enteric nervous system development relies on intestinal colonization by enteric neural crest-derived cells (ENCDCs). This is driven by a population of highly migratory and proliferative ENCDCs at the wavefront, but the molecular characteristics of these cells are unknown. ENCDCs from the wavefront and the trailing region were isolated and subjected to RNA-seq. Wavefront-ENCDCs were transcriptionally distinct from trailing ENCDCs, and temporal modelling confirmed their relative immaturity. This population of ENCDCs exhibited altered expression of ECM and cytoskeletal genes, consistent with a migratory phenotype. Unlike trailing ENCDCs, the wavefront lacked expression of genes related to neuronal or glial maturation. As wavefront ENCDC genes were associated with migration and developmental immaturity, the genes that remain expressed in later progenitor populations may be particularly pertinent to understanding the maintenance of ENCDC progenitor characteristics. Dusp6 expression was specifically upregulated at the wavefront. Inhibiting DUSP6 activity prevented wavefront colonization of the hindgut, and inhibited the migratory ability of post-colonized ENCDCs from midgut and postnatal neurospheres. These effects were reversed by simultaneous inhibition of ERK signaling, indicating that DUSP6-mediated ERK inhibition is required for ENCDC migration in mouse and chick.
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Affiliation(s)
- Rhian Stavely
- Department of Pediatric Surgery, Pediatric Surgery Research Laboratories, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ryo Hotta
- Department of Pediatric Surgery, Pediatric Surgery Research Laboratories, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Richard A. Guyer
- Department of Pediatric Surgery, Pediatric Surgery Research Laboratories, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Nicole Picard
- Department of Pediatric Surgery, Pediatric Surgery Research Laboratories, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ahmed A. Rahman
- Department of Pediatric Surgery, Pediatric Surgery Research Laboratories, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Meredith Omer
- Department of Pediatric Surgery, Pediatric Surgery Research Laboratories, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Adam Soos
- Department of Anatomy, Histology and Embryology, Faculty of Medicine, Semmelweis University, Budapest 1094, Hungary
| | - Emoke Szocs
- Department of Anatomy, Histology and Embryology, Faculty of Medicine, Semmelweis University, Budapest 1094, Hungary
| | - Jessica Mueller
- Department of Pediatric Surgery, Pediatric Surgery Research Laboratories, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Allan M. Goldstein
- Department of Pediatric Surgery, Pediatric Surgery Research Laboratories, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Nandor Nagy
- Department of Anatomy, Histology and Embryology, Faculty of Medicine, Semmelweis University, Budapest 1094, Hungary
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6
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Gattoni G, de la Haba RR, Martín J, Reyes F, Sánchez-Porro C, Feola A, Zuchegna C, Guerrero-Flores S, Varcamonti M, Ricca E, Selem-Mojica N, Ventosa A, Corral P. Genomic study and lipidomic bioassay of Leeuwenhoekiella parthenopeia: A novel rare biosphere marine bacterium that inhibits tumor cell viability. Front Microbiol 2023; 13:1090197. [PMID: 36687661 PMCID: PMC9859067 DOI: 10.3389/fmicb.2022.1090197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 12/09/2022] [Indexed: 01/09/2023] Open
Abstract
The fraction of low-abundance microbiota in the marine environment is a promising target for discovering new bioactive molecules with pharmaceutical applications. Phenomena in the ocean such as diel vertical migration (DVM) and seasonal dynamic events influence the pattern of diversity of marine bacteria, conditioning the probability of isolation of uncultured bacteria. In this study, we report a new marine bacterium belonging to the rare biosphere, Leeuwenhoekiella parthenopeia sp. nov. Mr9T, which was isolated employing seasonal and diel sampling approaches. Its complete characterization, ecology, biosynthetic gene profiling of the whole genus Leeuwenhoekiella, and bioactivity of its extract on human cells are reported. The phylogenomic and microbial diversity studies demonstrated that this bacterium is a new and rare species, barely representing 0.0029% of the bacterial community in Mediterranean Sea metagenomes. The biosynthetic profiling of species of the genus Leeuwenhoekiella showed nine functionally related gene cluster families (GCF), none were associated with pathways responsible to produce known compounds or registered patents, therefore revealing its potential to synthesize novel bioactive compounds. In vitro screenings of L. parthenopeia Mr9T showed that the total lipid content (lipidome) of the cell membrane reduces the prostatic and brain tumor cell viability with a lower effect on normal cells. The lipidome consisted of sulfobacin A, WB 3559A, WB 3559B, docosenamide, topostin B-567, and unknown compounds. Therefore, the bioactivity could be attributed to any of these individual compounds or due to their synergistic effect. Beyond the rarity and biosynthetic potential of this bacterium, the importance and novelty of this study is the employment of sampling strategies based on ecological factors to reach the hidden microbiota, as well as the use of bacterial membrane constituents as potential novel therapeutics. Our findings open new perspectives on cultivation and the relationship between bacterial biological membrane components and their bioactivity in eukaryotic cells, encouraging similar studies in other members of the rare biosphere.
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Affiliation(s)
- Giuliano Gattoni
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | | | | | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Antonia Feola
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Candida Zuchegna
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Shaday Guerrero-Flores
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México (UNAM), Morelia, Mexico
| | - Mario Varcamonti
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Ezio Ricca
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Nelly Selem-Mojica
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México (UNAM), Morelia, Mexico
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Paulina Corral
- Department of Biology, University of Naples Federico II, Naples, Italy,Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain,*Correspondence: Paulina Corral,
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7
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Caglar HO, Duzgun Z. Identification of upregulated genes in glioblastoma and glioblastoma cancer stem cells using bioinformatics analysis. Gene X 2023; 848:146895. [DOI: 10.1016/j.gene.2022.146895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/10/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022] Open
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8
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Guler S, Zik B, Yalcin A. Upregulation of dual-specificity phosphatase-26 is required for transforming growth factor β1(TGFβ1)-induced Epithelial-mesenchymal transition in A549 and PANC1 cells. Mol Biol Rep 2022; 49:10195-10204. [PMID: 36053282 DOI: 10.1007/s11033-022-07893-1] [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: 05/30/2022] [Accepted: 08/19/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND Transforming Growth Factor β (TGFβ) proteins are potent inducers of the epithelial-mesenchymal transition (EMT) in tumor cells. Although mitogen-activated protein kinase (MAPK) family has been shown to be involved in TGFβ-induced EMT, role of Dual Specificity Phosphatases (DUSP), key regulators of MAPK activity, in TGFβ-induced EMT is largely unkonwn. METHODS AND RESULTS Real-time qPCR analyses were performed to determine the effect of TGFβ1 on expression of EMT genes and DUSP proteins in the non-small cell lung cancer model A549 and pancreatic adenocarcinoma model PANC1 cells. Western blot analyses were conducted to study the changes in protein levels of EMT proteins and select DUSP proteins, as well as phosphorylations of MAPK proteins upon TGFβ1 stimulation. Small interfering RNA (siRNA) was utilized to reduce expressions of DUSP genes. We observed that the EMT phenotype coincided with increases in phosphorylations of the MAPK proteins ERK1/2, p38MAPK, and JNK upon TGFβ1 stimulation. Real-time qPCR analysis showed increases in DUSP15 and DUSP26 mRNA levels and Western blot analysis confirmed the increase in DUSP26 protein levels in both A549 and PANC1 cells treated with TGFβ1 relative to control. Silencing of DUSP26 expression by siRNA markedly suppressed the effect of TGFβ1 on E-cadherin and mesenchymal genes in the cells. CONCLUSIONS Data provided suggest that TGFβ1 modulates the expression of DUSP genes and that upregulation of DUSP26 may be required for TGFβ1-promoted EMT in A549 and PANC1 cells. Further studies should be carried out to elucidate the requirement of individual DUSPs in TGFβ1-associated EMT in tumor cells.
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Affiliation(s)
- Sabire Guler
- Department of Histology & Embryology, School of Veterinary Medicine, Bursa Uludag University, 16059, Bursa, Turkey
| | - Berrin Zik
- Department of Histology & Embryology, School of Veterinary Medicine, Bursa Uludag University, 16059, Bursa, Turkey
| | - Abdullah Yalcin
- Department of Biochemistry, School of Veterinary Medicine, Bursa Uludag University, 16059, Bursa, Turkey.
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9
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Nagashima Y, Nishimura Y, Eguchi K, Yamaguchi J, Haimoto S, Ohka F, Takayasu M, Saito R. Recent Molecular and Genetic Findings in Intramedullary Spinal Cord Tumors. Neurospine 2022; 19:262-271. [PMID: 35577330 PMCID: PMC9260550 DOI: 10.14245/ns.2244168.084] [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: 02/28/2022] [Accepted: 03/09/2022] [Indexed: 11/19/2022] Open
Abstract
The study of genetic alterations and molecular biology in central nervous system (CNS) tumors has improved the accuracy of estimations of patient prognosis and tumor categorization. Therefore, the updated 2021 World Health Organization (WHO) classification includes various diagnostic genes, molecules, and pathways for diagnosis, as well as histological findings. These findings are expected both to have diagnostic applications and to facilitate new targeted therapies that target tumor-specific genetic changes and molecular biology. Intramedullary spinal cord tumors (IMSCTs) are rare CNS tumors that are difficult to treat because they occur in eloquent areas. Although the genetic underpinnings of IMSCTs remain unclear compared to their intracranial counterparts, the genetic characteristics of these tumors are gradually being revealed. Here, we describe the major changes in the new 2021 WHO classification and review the major types of IMSCTs, with an emphasis on their clinical features and genetic alterations.
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Affiliation(s)
- Yoshitaka Nagashima
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya, Japan
| | - Yusuke Nishimura
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya, Japan
- Corresponding Author Yusuke Nishimura Department of Neurosurgery, Nagoya University School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8560, Japan
| | - Kaoru Eguchi
- Department of Neurosurgery, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Junya Yamaguchi
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya, Japan
| | - Shoichi Haimoto
- Department of Neurosurgery, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Fumiharu Ohka
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya, Japan
| | - Masakazu Takayasu
- Department of Neurosurgery, Inazawa Municipal Hospital, Aichi, Japan
| | - Ryuta Saito
- Department of Neurosurgery, Nagoya University School of Medicine, Nagoya, Japan
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10
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Kalya MP, Beisbarth T, Kel A. [Master regulators associated with poor prognosis in glioblastoma multiforme]. BIOMEDITSINSKAIA KHIMIIA 2021; 67:201-212. [PMID: 34142527 DOI: 10.18097/pbmc20216703201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Glioblastoma multiforme (GBM) is a highly malignant brain tumor with average survival time of 15 months. Less than 2% of the patients survive beyond 36 months. To understand the molecular mechanism responsible for poor prognosis, we analyzed GBM samples of TCGA microarray (n=560) data. We have identified 720 genes that have a significant impact upon survival based on univariate cox regression. We applied the Genome Enhancer pipeline to analyze potential mechanisms of regulation of activity of these genes and to build gene regulatory networks. We identified 12 transcription factors enriched in the promoters of these genes including the key molecule of GBM - STAT3. We found that STAT3 had significant differential expression across extreme survivor groups (short-term survivors- survival 36 months) and also had a significant impact on survival. In the next step, we identified master regulators in the signal transduction network that regulate the activity of these transcription factors. Master regulators are filtered based on their differential expression across extreme survivors groups and impact on survival. This work validates our earlier report on master regulators IGFBP2, PDGFA, OSMR, and AEBP1 driving short survival. Additionally, we propose CD14, CD44, DUSP6, GRB10, IL1RAP, FGFR3, and POSTN as master regulators driving poor survival. These master regulators are proposed as promising therapeutic targets to counter poor prognosis in GBM. Finally, the algorithm has prioritized several drugs for the further study as potential remedies to conquer the aggressive forms of GBM and to extend survival of the patients.
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Affiliation(s)
- M P Kalya
- University Medical Center Göttingen, Göttingen, Germany; geneXplain GmbH, Wolfenbüttel, Germany
| | - T Beisbarth
- University Medical Center Göttingen, Göttingen, Germany
| | - A Kel
- geneXplain GmbH, Wolfenbüttel, Germany; Institute of Chemical Biology and Fundamental Medicine SBRAS, Novosibirsk, Russia
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Kanda Y, Mizuno A, Takasaki T, Satoh R, Hagihara K, Masuko T, Endo Y, Tanabe G, Sugiura R. Down-regulation of dual-specificity phosphatase 6, a negative regulator of oncogenic ERK signaling, by ACA-28 induces apoptosis in NIH/3T3 cells overexpressing HER2/ErbB2. Genes Cells 2020; 26:109-116. [PMID: 33249692 DOI: 10.1111/gtc.12823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/20/2020] [Accepted: 11/21/2020] [Indexed: 12/15/2022]
Abstract
Dual-specificity phosphatase 6 (DUSP6) is a key negative feedback regulator of the member of the RAS-ERK MAPK signaling pathway that is associated with cellular proliferation and differentiation. Deterioration of DUSP6 expression could therefore result in deregulated growth activity. We have previously discovered ACA-28, a novel anticancer compound with a unique property to stimulate ERK phosphorylation and induce apoptosis in ERK-active melanoma cells. However, the mechanism of cancer cell-specific-apoptosis by ACA-28 remains obscure. Here, we investigated the involvement of DUSP6 in the mechanisms of the ACA-28-mediated apoptosis by using the NIH/3T3 cells overexpressing HER2/ErbB2 (A4-15 cells), as A4-15 exhibited higher ERK phosphorylation and are more susceptible to ACA-28 than NIH/3T3. We showed that A4-15 exhibited high DUSP6 protein levels, which require ERK activation. Notably, the silencing of the DUDSP6 gene by siRNA inhibited proliferation and induced apoptosis in A4-15, but not in NIH/3T3, indicating that A4-15 requires high DUSP6 expression for growth. Importantly, ACA-28 preferentially down-regulated the DUSP6 protein and proliferation in A4-15 via the proteasome, while it stimulated ERK phosphorylation. Collectively, the up-regulation of DUSP6 may exert a growth-promoting role in cancer cells overexpressing HER2. DUSP6 down-regulation in ERK-active cancer cells might have the potential as a novel cancer measure.
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Affiliation(s)
- Yuki Kanda
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Kindai University, Higashi-Osaka, Japan
| | - Ayami Mizuno
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Kindai University, Higashi-Osaka, Japan
| | - Teruaki Takasaki
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Kindai University, Higashi-Osaka, Japan
| | - Ryosuke Satoh
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Kindai University, Higashi-Osaka, Japan
| | - Kanako Hagihara
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Kindai University, Higashi-Osaka, Japan
| | - Takashi Masuko
- Laboratory of Natural Drug Resources, Department of Pharmaceutical Sciences, Kindai University, Higashi-Osaka, Japan
| | - Yuichi Endo
- Laboratory of Natural Drug Resources, Department of Pharmaceutical Sciences, Kindai University, Higashi-Osaka, Japan
| | - Genzoh Tanabe
- Laboratory of Organic Chemistry, Department of Pharmacy, Kindai University, Higashi-Osaka, Japan
| | - Reiko Sugiura
- Laboratory of Molecular Pharmacogenomics, Department of Pharmaceutical Sciences, Kindai University, Higashi-Osaka, Japan.,Pharmaceutical Research and Technology Institute, Kindai University, Higashi-Osaka, Japan
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