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Avşar G, Pir P. An integrated study to decipher immunosuppressive cellular communication in the PDAC environment. NPJ Syst Biol Appl 2023; 9:56. [PMID: 37945567 PMCID: PMC10636193 DOI: 10.1038/s41540-023-00320-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one the most aggressive cancers and characterized by a highly rigid and immunosuppressive tumor microenvironment (TME). The extensive cellular interactions are known to play key roles in the immune evasion, chemoresistance, and poor prognosis. Here, we used the spatial transcriptomics, scRNA-seq, and bulk RNA-seq datasets to enhance the insights obtained from each to decipher the cellular communication in the TME. The complex crosstalk in PDAC samples was revealed by the single-cell and spatial transcriptomics profiles of the samples. We show that tumor-associated macrophages (TAMs) are the central cell types in the regulation of microenvironment in PDAC. They colocalize with the cancer cells and tumor-suppressor immune cells and take roles to provide an immunosuppressive environment. LGALS9 gene which is upregulated in PDAC tumor samples in comparison to healthy samples was also found to be upregulated in TAMs compared to tumor-suppressor immune cells in cancer samples. Additionally, LGALS9 was found to be the primary component in the crosstalk between TAMs and the other cells. The widespread expression of P4HB gene and its interaction with LGALS9 was also notable. Our findings point to a profound role of TAMs via LGALS9 and its interaction with P4HB that should be considered for further elucidation as target in the combinatory immunotherapies for PDAC.
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Affiliation(s)
- Gülben Avşar
- Department of Bioengineering, Gebze Technical University, Kocaeli, Turkey.
- Turkish Academy of Sciences, Ankara, Turkey.
| | - Pınar Pir
- Department of Bioengineering, Gebze Technical University, Kocaeli, Turkey
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2
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Saeedifar AM, Ghazavi A, Mosayebi G, Ganji A. Synergistic apoptotic effects of ethanolic extracts of ginger and Ganoderma lucidum in a colorectal cancer cell line. Biotech Histochem 2023; 98:353-359. [PMID: 36970755 DOI: 10.1080/10520295.2023.2190620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Current conventional therapy for colorectal cancer includes surgery, radiation and chemotherapy, all of which produce side effects. Herbal medicine can control the side effects of conventional treatments. We investigated the synergistic effect of a mixture of Zingiber officinale Roscoe (Ginger) and Ganoderma lucidum extracts on colorectal cancer cell apoptosis in vitro. We prepared ethanolic extracts of ginger (GEE) and G. lucidum (GLEE). Cytotoxicity was evaluated using MTT assay and the half-maximal inhibitory concentration (IC50) of each extract was calculated. The effect of these extracts on apoptosis in cancer cells was assessed using flow cytometry; Bax, Bcl2 and caspase-3 gene expression was evaluated using real-time PCR. GEE and GLEE decreased CT-26 cell viability significantly in a dose-dependent manner; however, the combined application of GEE + GLEE was most effective. Bax:Bcl-2 gene expression ratio, caspase-3 gene expression and the number of apoptotic cells were increased significantly in CT-26 cells treated at the IC50 level of each compound, especially in the GEE + GLEE treatment group. Combined ginger and Ganoderma lucidum extracts exhibited synergistic antiproliferative and apoptotic effects on colorectal cancer cells.
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Affiliation(s)
- Amir Mohammad Saeedifar
- Student Research Committee, Arak University of Medical Sciences, Arak, Iran
- Department of Immunology, School of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Ali Ghazavi
- Department of Immunology, School of Medicine, Arak University of Medical Sciences, Arak, Iran
- Traditional and Complementary Medicine Research Center (TCMRC), Arak University of Medical Sciences, Arak, Iran
| | - Ghasem Mosayebi
- Department of Immunology, School of Medicine, Arak University of Medical Sciences, Arak, Iran
- Molecular and Medicine Research Center, Arak University of Medical Sciences, Arak, Iran
| | - Ali Ganji
- Department of Immunology, School of Medicine, Arak University of Medical Sciences, Arak, Iran
- Molecular and Medicine Research Center, Arak University of Medical Sciences, Arak, Iran
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Park CY, Jang JH, Song IH, Kim JY, Doh KO, Lee TJ. Suppression of TBCK enhances TRAIL-mediated apoptosis by causing the inactivation of the akt signaling pathway in human renal carcinoma Caki-1 cells. Genes Genomics 2023; 45:1357-1365. [PMID: 37725269 DOI: 10.1007/s13258-023-01453-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/29/2023] [Indexed: 09/21/2023]
Abstract
BACKGROUND TBC1 domain-containing kinase (TBCK) protein functions as a growth suppressor in certain cell types and as a tumor promoter in others. Although TBCK knockdown increases the responsiveness of cancer cells to anticancer drugs, the detailed mechanisms by which TBCK knockdown increases susceptibility to anticancer drugs remain unknown. OBJECTIVE This study analyzed the role of TBCK in sensitivities to tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and doxorubicin in human renal cancer cells. METHODS Flow cytometry was employed to evaluate the extent of apoptosis. Western blotting, transient transfection, and lentiviral infection techniques were conducted to investigate the impact of TBCK on apoptosis-related protein expression and mitogen-activated protein kinase (MAPK). RESULTS TBCK knockdown in renal cancer cells inhibits ERK and Akt signaling pathways and increases TRAIL and doxorubicin sensitivity. In TBCK-knockdown Caki-1 cells, ERK and Akt phosphorylation was suppressed compared to control cell lines, and TRAIL and doxorubicin sensitivities were increased in these cells. In addition, the phosphorylation of PDK1 was suppressed in TBCK-suppressed cells, indicating that TBCK may be involved in the PDK1 and Akt signaling pathways. The introduction of dominantly active Akt into TBCK-suppressed cells restored their sensitivity to TRAIL. In addition, TBCK downregulation enhanced TRAIL sensitivity in different renal cancer cell lines. CONCLUSIONS These data suggest that TBCK could potentially have a crucial function in influencing the effects of anti-cancer drugs including TRAIL by modulating the signaling pathway involving Akt and PDK1 in human renal cancer cells.
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Affiliation(s)
- Cho-Young Park
- Department of Anatomy, College of Medicine, Yeungnam University, 170 Hyeonchung-ro, Nam-Gu, Daegu, 705- 717, Korea
| | - Ji-Hoon Jang
- Department of Anatomy, College of Medicine, Yeungnam University, 170 Hyeonchung-ro, Nam-Gu, Daegu, 705- 717, Korea
| | - In-Hwan Song
- Department of Anatomy, College of Medicine, Yeungnam University, 170 Hyeonchung-ro, Nam-Gu, Daegu, 705- 717, Korea
| | - Joo-Young Kim
- Department of Anatomy, College of Medicine, Yeungnam University, 170 Hyeonchung-ro, Nam-Gu, Daegu, 705- 717, Korea
| | - Kyung-Oh Doh
- Department of Physiology, College of Medicine, Yeungnam University, 170 Hyeonchung-ro, Nam-Gu, Daegu, 705-717, Korea
| | - Tae-Jin Lee
- Department of Anatomy, College of Medicine, Yeungnam University, 170 Hyeonchung-ro, Nam-Gu, Daegu, 705- 717, Korea.
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4
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Durham EL, Angireddy R, Black A, Melendez-Perez A, Smith S, Gonzalez EM, Navarro KG, Díaz A, Bhoj EJK, Katsura KA. TBCK syndrome: a rare multi-organ neurodegenerative disease. Trends Mol Med 2023; 29:783-785. [PMID: 37455236 PMCID: PMC10868401 DOI: 10.1016/j.molmed.2023.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023]
Abstract
TBCK syndrome is an autosomal recessive disorder primarily characterized by global developmental delay, hypotonia, abnormal magnetic resonance imaging (MRI), and distinctive craniofacial phenotypes. High variability is observed among affected individuals and their corresponding variants, making clinical diagnosis challenging. Here, we discuss recent breakthroughs in clinical considerations, TBCK function, and therapeutic development.
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Affiliation(s)
- Emily L Durham
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, PA, USA
| | - Rajesh Angireddy
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, PA, USA
| | - Aaron Black
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, PA, USA
| | - Ashley Melendez-Perez
- Division of Human Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Sarina Smith
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, PA, USA
| | - Elizabeth M Gonzalez
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, PA, USA; Division of Human Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Kristen G Navarro
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, PA, USA
| | - Abdias Díaz
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, PA, USA; Division of Human Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth J K Bhoj
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, PA, USA; Division of Human Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
| | - Kaitlin A Katsura
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, PA, USA; Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA.
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5
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An Updated Review of Contribution of Long Noncoding RNA-NEAT1 to the Progression of Human Cancers. Pathol Res Pract 2023; 245:154380. [PMID: 37043964 DOI: 10.1016/j.prp.2023.154380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/12/2023] [Accepted: 02/16/2023] [Indexed: 02/26/2023]
Abstract
Long non-coding RNAs (lncRNAs) present pivotal roles in cancer tumorigenesis and progression. Recently, nuclear paraspeckle assembly transcript 1 (NEAT1) as a lncRNA has been shown to mediate cell proliferation, migration, and EMT in tumor cells. NEAT1 by targeting several miRNAs/mRNA axes could regulate cancer cell behavior. Therefore, NEAT1 may function as a potent biomarker for the prediction and treatment of some human cancers. In this review, we summarized various NEAT1-related signaling pathways that are critical in cancer initiation and progression.
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Zhu Y, Liu Z, Guo Y, Li S, Qu Y, Dai L, Chen Y, Ning W, Zhang H, Ma L. Whole-genome sequencing of extrachromosomal circular DNA of cerebrospinal fluid of medulloblastoma. Front Oncol 2022; 12:934159. [PMID: 36452490 PMCID: PMC9703567 DOI: 10.3389/fonc.2022.934159] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 10/12/2022] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Medulloblastoma (MB) is a malignant tumor associated with a poor prognosis in part due to a lack of effective detection methods. Extrachromosomal circular DNA (eccDNA) has been associated with multiple tumors. Nonetheless, little is currently known on eccDNA in MB. METHODS Genomic features of eccDNAs were identified in MB tissues and matched cerebrospinal fluid (CSF) and compared with corresponding normal samples using Circle map. The nucleotides on both sides of the eccDNAs' breakpoint were analyzed to understand the mechanisms of eccDNA formation. Bioinformatics analysis combined with the Gene Expression Omnibus (GEO) database identified features of eccDNA-related genes in MB. Lasso Cox regression model, univariate and multivariate Cox regression analysis, time-dependent ROC, and Kaplan-Meier curve were used to assess the potential diagnostic and prognostic value of the hub genes. RESULTS EccDNA was profiled in matched tumor and CSF samples from MB patients, and control, eccDNA-related genes enriched in MB were identified. The distribution of eccDNAs in the genome was closely related to gene density and the mechanism of eccDNA formation was evaluated. EccDNAs in CSF exhibited similar distribution with matched MB tissues but were differentially expressed between tumor and normal. Ten hub genes prominent in both the eccDNA dataset and the GEO database were selected to classify MB patients to either high- or low-risk groups, and a prognostic nomogram was thus established. CONCLUSIONS This study provides preliminary evidence of the characteristics and formation mechanism of eccDNAs in MB and CSF. Importantly, eccDNA-associated hub genes in CSF could be used as diagnostic and prognostic biomarkers for MB.
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Affiliation(s)
- Yi Zhu
- Department of Neurosurgery, Binzhou Medical University Hospital, Binzhou, China
| | - Zhihui Liu
- Department of Obstetrics and Gynecology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Yuduo Guo
- Chinese Academy of Sciences (CAS) Key Laboratory of Infection and Immunity, Institute of biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shenglun Li
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Yanming Qu
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Lin Dai
- Department of Neurosurgery, Binzhou Medical University Hospital, Binzhou, China
| | - Yujia Chen
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Weihai Ning
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Hongwei Zhang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Lixin Ma
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
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Lee S, Osmanbeyoglu HU. Chromatin accessibility landscape and active transcription factors in primary human invasive lobular and ductal breast carcinomas. BREAST CANCER RESEARCH : BCR 2022; 24:54. [PMID: 35906698 PMCID: PMC9338552 DOI: 10.1186/s13058-022-01550-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/25/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Invasive lobular breast carcinoma (ILC), the second most prevalent histological subtype of breast cancer, exhibits unique molecular features compared with the more common invasive ductal carcinoma (IDC). While genomic and transcriptomic features of ILC and IDC have been characterized, genome-wide chromatin accessibility pattern differences between ILC and IDC remain largely unexplored. METHODS Here, we characterized tumor-intrinsic chromatin accessibility differences between ILC and IDC using primary tumors from The Cancer Genome Atlas (TCGA) breast cancer assay for transposase-accessible chromatin with sequencing (ATAC-seq) dataset. RESULTS We identified distinct patterns of genome-wide chromatin accessibility in ILC and IDC. Inferred patient-specific transcription factor (TF) motif activities revealed regulatory differences between and within ILC and IDC tumors. EGR1, RUNX3, TP63, STAT6, SOX family, and TEAD family TFs were higher in ILC, while ATF4, PBX3, SPDEF, PITX family, and FOX family TFs were higher in IDC. CONCLUSIONS This study reveals the distinct epigenomic features of ILC and IDC and the active TFs driving cancer progression that may provide valuable information on patient prognosis.
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Affiliation(s)
- Sanghoon Lee
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, USA.,UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA
| | - Hatice Ulku Osmanbeyoglu
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, USA. .,Department of Bioengineering, School of Engineering, University of Pittsburgh, Pittsburgh, USA. .,UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA. .,Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, USA.
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Kesheh MM, Mahmoudvand S, Shokri S. Long noncoding RNAs in respiratory viruses: A review. Rev Med Virol 2021; 32:e2275. [PMID: 34252234 PMCID: PMC8420315 DOI: 10.1002/rmv.2275] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 06/26/2021] [Accepted: 06/29/2021] [Indexed: 12/27/2022]
Abstract
Long noncoding RNAs (lncRNAs) are defined as RNA molecules longer than 200 nucleotides that can regulate gene expression at the transcriptional or post‐transcriptional levels. Both human lncRNAs and lncRNAs encoded by viruses can modulate the expression of host genes which are critical for viral replication, latency, activation of signalling pathways, cytokine and chemokine production, RNAi processing, expression of interferons (IFNs) and interferon‐stimulated genes (ISGs). Studies on lncRNAs as key regulators of host‐virus interactions may give new insights into therapeutic strategies for the treatment of related diseases. This current review focuses on the role of lncRNAs, and their interactions with respiratory viruses including influenza A virus (IAV), respiratory syncytial virus (RSV) and severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2).
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Affiliation(s)
- Mina Mobini Kesheh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shahab Mahmoudvand
- Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Somayeh Shokri
- Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Dieterle MP, Husari A, Steinberg T, Wang X, Ramminger I, Tomakidi P. From the Matrix to the Nucleus and Back: Mechanobiology in the Light of Health, Pathologies, and Regeneration of Oral Periodontal Tissues. Biomolecules 2021; 11:824. [PMID: 34073044 PMCID: PMC8228498 DOI: 10.3390/biom11060824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 02/07/2023] Open
Abstract
Among oral tissues, the periodontium is permanently subjected to mechanical forces resulting from chewing, mastication, or orthodontic appliances. Molecularly, these movements induce a series of subsequent signaling processes, which are embedded in the biological concept of cellular mechanotransduction (MT). Cell and tissue structures, ranging from the extracellular matrix (ECM) to the plasma membrane, the cytosol and the nucleus, are involved in MT. Dysregulation of the diverse, fine-tuned interaction of molecular players responsible for transmitting biophysical environmental information into the cell's inner milieu can lead to and promote serious diseases, such as periodontitis or oral squamous cell carcinoma (OSCC). Therefore, periodontal integrity and regeneration is highly dependent on the proper integration and regulation of mechanobiological signals in the context of cell behavior. Recent experimental findings have increased the understanding of classical cellular mechanosensing mechanisms by both integrating exogenic factors such as bacterial gingipain proteases and newly discovered cell-inherent functions of mechanoresponsive co-transcriptional regulators such as the Yes-associated protein 1 (YAP1) or the nuclear cytoskeleton. Regarding periodontal MT research, this review offers insights into the current trends and open aspects. Concerning oral regenerative medicine or weakening of periodontal tissue diseases, perspectives on future applications of mechanobiological principles are discussed.
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Affiliation(s)
- Martin Philipp Dieterle
- Center for Dental Medicine, Division of Oral Biotechnology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany; (M.P.D.); (X.W.); (I.R.); (P.T.)
| | - Ayman Husari
- Center for Dental Medicine, Department of Orthodontics, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany;
- Faculty of Engineering, University of Freiburg, Georges-Köhler-Allee 101, 79110 Freiburg, Germany
| | - Thorsten Steinberg
- Center for Dental Medicine, Division of Oral Biotechnology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany; (M.P.D.); (X.W.); (I.R.); (P.T.)
| | - Xiaoling Wang
- Center for Dental Medicine, Division of Oral Biotechnology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany; (M.P.D.); (X.W.); (I.R.); (P.T.)
| | - Imke Ramminger
- Center for Dental Medicine, Division of Oral Biotechnology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany; (M.P.D.); (X.W.); (I.R.); (P.T.)
| | - Pascal Tomakidi
- Center for Dental Medicine, Division of Oral Biotechnology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Hugstetterstr. 55, 79106 Freiburg, Germany; (M.P.D.); (X.W.); (I.R.); (P.T.)
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Zhou C, Li AH, Liu S, Sun H. Identification of an 11-Autophagy-Related-Gene Signature as Promising Prognostic Biomarker for Bladder Cancer Patients. BIOLOGY 2021; 10:biology10050375. [PMID: 33925460 PMCID: PMC8146553 DOI: 10.3390/biology10050375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/17/2021] [Accepted: 04/23/2021] [Indexed: 12/15/2022]
Abstract
Simple Summary Human bladder cancer, one of the most common cancers worldwide, is a molecularly heterogenous and complex disease. Identifying novel prognostic biomarkers and establishing new predictive signatures are important for personalized medicine and effective treatment of bladder cancer patients. Autophagy, a cell self-maintenance process that removes damaged organelles and misfolded proteins, displays both tumor promotion and suppression activities. The aim of our study is to investigate the function of autophagy-related genes in bladder cancer with the main focus on their contribution to prognostic outcome. By analyzing data obtained from The Cancer Genome Atlas (TCGA), we identified 32 autophagy-related genes that were highly associated with overall survival of bladder cancer patients. Further statistical assessment established an 11-autophagy-related-gene signature as an effective prognostic biomarker to predict the survival outcomes of bladder cancer patients. Abstract Background: Survival rates for highly invasive bladder cancer (BC) patients have been very low, with a 5-year survival rate of 6%. Accurate prediction of tumor progression and survival is important for diagnosis and therapeutic decisions for BC patients. Our study aims to develop an autophagy-related-gene (ARG) signature that helps to predict the survival of BC patients. Methods: RNA-seq data of 403 BC patients were retrieved from The Cancer Genome Atlas Urothelial Bladder Carcinoma (TCGA-BLCA) database. Univariate Cox regression analysis was performed to identify overall survival (OS)-related ARGs. The Lasso Cox regression model was applied to establish an ARG signature in the TCGA training cohort (N = 203). The performance of the 11-gene ARG signature was further evaluated in a training cohort and an independent validation cohort (N = 200) using Kaplan-Meier OS curve analysis, receiver operating characteristic (ROC) analysis, as well as univariate and multivariate Cox regression analysis. Results: Our study identified an 11-gene ARG signature that is significantly associated with OS, including APOL1, ATG4B, BAG1, CASP3, DRAM1, ITGA3, KLHL24, P4HB, PRKCD, ULK2, and WDR45. The ARGs-derived high-risk bladder cancer patients exhibited significantly poor OS in both training and validation cohorts. The prognostic model showed good predictive efficacy, with the area under the ROC curve (AUCs) for 1-year, 3-year, and 5-year overall survival of 0.702 (0.695), 0.744 (0.640), and 0.794 (0.658) in the training and validation cohorts, respectively. A prognostic nomogram, which included the ARGs-derived risk factor, age and stage for eventual clinical translation, was established. Conclusion: We identified a novel ARG signature for risk-stratification and robust prediction of overall survival for BC patients.
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Affiliation(s)
| | | | | | - Hong Sun
- Correspondence: ; Tel.: +1-(646)-754-9459
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Lai X, Wei J, Gu XZ, Yao XM, Zhang DS, Li F, Sun YY. Dysregulation of LINC00470 and METTL3 promotes chemoresistance and suppresses autophagy of chronic myelocytic leukaemia cells. J Cell Mol Med 2021; 25:4248-4259. [PMID: 33749070 PMCID: PMC8093980 DOI: 10.1111/jcmm.16478] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 12/12/2022] Open
Abstract
Cytoplasmic lncRNAs have been found to directly interact with target mRNAs and regulate their stability. In this study, we aimed to study the molecular mechanism underlying the function of m6 A as a central regulator in chemoresistance and CML proliferation. In this study, we established three mice groups (control group, ADR-R group and ADR-R + shLINC00470 group). We detected PTEN mRNA expression in the presence of LINC00470 in the mice models, as well as in the KCL22 and K562 cells. LINC00470 was significantly enriched for PTEN mRNA to exhibit a negative regulatory relationship between LINC00470 and PTEN mRNA. However, the alteration of LINC00470 had no effect on the luciferase activity of PTEN promoter, while the half-life of PTEN mRNA was affected. It was further validated that LINC00470 down-regulated PTEN expression by positively regulating the m6A modification of PTEN mRNA via RNA methyltransferase METTL3. Moreover, the relative expression of LC3II, Beclin-1, ATG7 and ATG5 was all decreased in cells treated with LINC00470, and down-regulated PTEN expression was observed in chemo-resistant cells, while the expression of PTEN was rescued by the transfection of shMETTL3 into chemo-resistant cells. Moreover, the knockdown of METTL3 also restored the normal level of PTEN m6 A modification and LINC00470 expression in chemo-resistant cells. In conclusion, our results demonstrated the molecular mechanism underlying the effect of LINC00470 on CML by reducing the PTEN stability via RNA methyltransferase METTL3, thus leading to the inhibition of cell autophagy while promoting chemoresistance in CML.
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Affiliation(s)
- Xun Lai
- Department of Hematology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, China
| | - Jia Wei
- Department of Hematology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, China
| | - Xue-Zhong Gu
- Department of Hematology, The First People's Hospital of Yunnan Province, Kunming, China
| | - Xiang-Mei Yao
- Department of Hematology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, China
| | - Di-Si Zhang
- Department of Hematology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, China
| | - Feng Li
- Department of Hematology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, China
| | - Yun-Yan Sun
- Department of Hematology, The Third Affiliated Hospital of Kunming Medical University (Tumor Hospital of Yunnan Province), Kunming, China
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