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Li Z, Ma Z, Xue H, Shen R, Qin K, Zhang Y, Zheng X, Zhang G. Chromatin Separation Regulators Predict the Prognosis and Immune Microenvironment Estimation in Lung Adenocarcinoma. Front Genet 2022; 13:917150. [PMID: 35873497 PMCID: PMC9305311 DOI: 10.3389/fgene.2022.917150] [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: 04/11/2022] [Accepted: 05/23/2022] [Indexed: 11/24/2022] Open
Abstract
Background: Abnormal chromosome segregation is identified to be a common hallmark of cancer. However, the specific predictive value of it in lung adenocarcinoma (LUAD) is unclear. Method: The RNA sequencing and the clinical data of LUAD were acquired from The Cancer Genome Atlas (TACG) database, and the prognosis-related genes were identified. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) were carried out for functional enrichment analysis of the prognosis genes. The independent prognosis signature was determined to construct the nomogram Cox model. Unsupervised clustering analysis was performed to identify the distinguishing clusters in LUAD-samples based on the expression of chromosome segregation regulators (CSRs). The differentially expressed genes (DEGs) and the enriched biological processes and pathways between different clusters were identified. The immune environment estimation, including immune cell infiltration, HLA family genes, immune checkpoint genes, and tumor immune dysfunction and exclusion (TIDE), was assessed between the clusters. The potential small-molecular chemotherapeutics for the individual treatments were predicted via the connectivity map (CMap) database. Results: A total of 2,416 genes were determined as the prognosis-related genes in LUAD. Chromosome segregation is found to be the main bioprocess enriched by the prognostic genes. A total of 48 CSRs were found to be differentially expressed in LUAD samples and were correlated with the poor outcome in LUAD. Nine CSRs were identified as the independent prognostic signatures to construct the nomogram Cox model. The LUAD-samples were divided into two distinct clusters according to the expression of the 48 CSRs. Cell cycle and chromosome segregation regulated genes were enriched in cluster 1, while metabolism regulated genes were enriched in cluster 2. Patients in cluster 2 had a higher score of immune, stroma, and HLA family components, while those in cluster 1 had higher scores of TIDES and immune checkpoint genes. According to the hub genes highly expressed in cluster 1, 74 small-molecular chemotherapeutics were predicted to be effective for the patients at high risk. Conclusion: Our results indicate that the CSRs were correlated with the poor prognosis and the possible immunotherapy resistance in LUAD.
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Affiliation(s)
- Zhaoshui Li
- Qingdao Medical College, Qingdao University, Qingdao, China
- Cardiothoracic Surgery Department, Qingdao Hiser Hospital Affiliated to Qingdao University, Qingdao, China
| | - Zaiqi Ma
- Cardiothoracic Surgery Department, Qingdao Hiser Hospital Affiliated to Qingdao University, Qingdao, China
| | - Hong Xue
- Heart Center Department, Qingdao Hiser Hospital Affiliated to Qingdao University, Qingdao, China
| | - Ruxin Shen
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Kun Qin
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Yu Zhang
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Xin Zheng
- Cancer Center Department, Qingdao Hiser Hospital Affiliated to Qingdao University, Qingdao, China
- *Correspondence: Xin Zheng, ; Guodong Zhang,
| | - Guodong Zhang
- Thoracic Surgery Department, Shandong Cancer Hospital Affiliated to Shandong First Medical University, Jinan, China
- *Correspondence: Xin Zheng, ; Guodong Zhang,
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Yu W, Zheng Z, Wei W, Li L, Zhang Y, Sun Y, Cao J, Zang W, Shao J. Raf1 interacts with OIP5 to participate in oxaliplatin-induced neuropathic pain. Life Sci 2021; 281:119804. [PMID: 34229010 DOI: 10.1016/j.lfs.2021.119804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/16/2021] [Accepted: 06/28/2021] [Indexed: 11/18/2022]
Abstract
AIMS Oxaliplatin is an effective anti-cancer platinum-based chemotherapy drug which can cause severe chronic neuropathy, but the molecular mechanism underlying this adverse effect is still unclear. Opa interacting protein 5 (OIP5) is a member of the cancer/testis antigen (CTA) family and is involved in a variety of cancers. Studies have shown that Raf1, which is a serine/threonine-protein kinase, can directly combine with OIP5 to promote its expression. Whether Raf1 and OIP5 can participate in oxaliplatin-induced neuropathic pain has not been reported. MAIN METHODS In this study, the oxaliplatin-induced neuropathic pain model was prepared by intraperitoneal injection of oxaliplatin. OIP5 and Raf1 were knocked down by intrathecal injection of siRNA against Raf1 and OIP5 (siRaf1, siOIP5). Von Frey fiber and acetone were used to detect pain behavior, and western blot was used to detect the protein expression changes of OIP5 and Raf1 in the dorsal root ganglion (DRG). KEY FINDINGS The expression levels of p-Raf1 and OIP5 were increased in DRGs of oxaliplatin-induced neuropathic pain rats. Intrathecal administration of siOIP5 to inhibit the expression of OIP5 not only effectively alleviated oxaliplatin-induced mechanical allodynia and cold hyperalgesia, but also decreased the protein expression of Raf1. Intrathecal administration of siRaf1 inhibited the expression of OIP5 and attenuated oxaliplatin-induced neuropathic pain. SIGNIFICANCE This study confirmed that Raf1 interacts with OIP5 to participate in oxaliplatin-induced neuropathic pain. The restricted expression of OIP5 in normal tissues may make it an ideal drug target for the treatment of oxaliplatin-induced neuropathic pain.
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Affiliation(s)
- Wenli Yu
- Department of Human Anatomy, School of Basic Medicine, Zhengzhou University, Zhengzhou 450001, China; Institute of Neuroscience, Zhengzhou University, Zhengzhou 450052, China
| | - Zhenli Zheng
- Department of Human Anatomy, School of Basic Medicine, Zhengzhou University, Zhengzhou 450001, China; Institute of Neuroscience, Zhengzhou University, Zhengzhou 450052, China
| | - Wei Wei
- Department of Human Anatomy, School of Basic Medicine, Zhengzhou University, Zhengzhou 450001, China; Institute of Neuroscience, Zhengzhou University, Zhengzhou 450052, China
| | - Lei Li
- Department of Human Anatomy, School of Basic Medicine, Zhengzhou University, Zhengzhou 450001, China; Institute of Neuroscience, Zhengzhou University, Zhengzhou 450052, China
| | - Yidan Zhang
- Department of Human Anatomy, School of Basic Medicine, Zhengzhou University, Zhengzhou 450001, China; Institute of Neuroscience, Zhengzhou University, Zhengzhou 450052, China
| | - Yanyan Sun
- Department of Human Anatomy, School of Basic Medicine, Zhengzhou University, Zhengzhou 450001, China; Institute of Neuroscience, Zhengzhou University, Zhengzhou 450052, China
| | - Jing Cao
- Department of Human Anatomy, School of Basic Medicine, Zhengzhou University, Zhengzhou 450001, China; Institute of Neuroscience, Zhengzhou University, Zhengzhou 450052, China
| | - Weidong Zang
- Department of Human Anatomy, School of Basic Medicine, Zhengzhou University, Zhengzhou 450001, China; Institute of Neuroscience, Zhengzhou University, Zhengzhou 450052, China
| | - Jinping Shao
- Department of Human Anatomy, School of Basic Medicine, Zhengzhou University, Zhengzhou 450001, China; Institute of Neuroscience, Zhengzhou University, Zhengzhou 450052, China.
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Wanowska E, Kubiak M, Makałowska I, Szcześniak MW. A chromatin-associated splicing isoform of OIP5-AS1 acts in cis to regulate the OIP5 oncogene. RNA Biol 2021; 18:1834-1845. [PMID: 33404283 PMCID: PMC8582974 DOI: 10.1080/15476286.2021.1871816] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A large portion of the human genome is transcribed into long noncoding RNAs that can range from 200 nucleotides to several kilobases in length. The number of identified lncRNAs is still growing, but only a handful of them have been functionally characterized. However, it is known that the functions of lncRNAs are closely related to their subcellular localization. Cytoplasmic lncRNAs can regulate mRNA stability, affect translation and act as miRNA sponges, while nuclear-retained long noncoding RNAs have been reported to be involved in transcriptional control, chromosome scaffolding, modulation of alternative splicing and chromatin remodelling. Through these processes, lncRNAs have diverse regulatory roles in cell biology and diseases. OIP5-AS1 (also known as Cyrano), a poorly characterized lncRNA expressed antisense to the OIP5 oncogene, is deregulated in multiple cancers. We showed that one of the OIP5-AS1 splicing forms (ENST00000501665.2) is retained in the cell nucleus where it associates with chromatin, thus narrowing down the spectrum of its possible mechanisms of action. Its knockdown with antisense LNA gapmeRs led to inhibited expression of a sense partner, OIP5, strongly suggesting a functional coupling between OIP5 and ENST00000501665.2. A subsequent bioinformatics analysis followed by RAP-MS and RNA Immunoprecipitation experiments suggested its possible mode of action; in particular, we found that ENST00000501665.2 directly binds to a number of nuclear proteins, including SMARCA4, a component of the SWI/SNF chromatin remodelling complex, whose binding motif is located in the promoter of the OIP5 oncogene.
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Affiliation(s)
- Elżbieta Wanowska
- Faculty of Biology, Adam Mickiewicz University in Poznan, Institute of Human Biology and Evolution, Uniwersytetu Poznańskiego 6, Poznan, Poland
| | - Magdalena Kubiak
- Faculty of Biology, Adam Mickiewicz University in Poznan, Institute of Human Biology and Evolution, Uniwersytetu Poznańskiego 6, Poznan, Poland
| | - Izabela Makałowska
- Faculty of Biology, Adam Mickiewicz University in Poznan, Institute of Human Biology and Evolution, Uniwersytetu Poznańskiego 6, Poznan, Poland
| | - Michał Wojciech Szcześniak
- Faculty of Biology, Adam Mickiewicz University in Poznan, Institute of Human Biology and Evolution, Uniwersytetu Poznańskiego 6, Poznan, Poland
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Rodrigues-Junior DM, Tan SS, Lim SK, Leong HS, Melendez ME, Ramos CRN, Viana LDS, Tan DSW, Carvalho AL, Iyer NG, Vettore AL. Circulating extracellular vesicle-associated TGFβ3 modulates response to cytotoxic therapy in head and neck squamous cell carcinoma. Carcinogenesis 2020; 40:1452-1461. [PMID: 31436806 DOI: 10.1093/carcin/bgz148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 08/14/2019] [Accepted: 08/20/2019] [Indexed: 01/28/2023] Open
Abstract
Management of locally advanced head and neck squamous cell carcinoma (HNSCC) requires a multi-prong approach comprising surgery, radiation and/or chemotherapy, yet outcomes are limited. This is largely due to a paucity of biomarkers that can predict response to specific treatment modalities. Here, we evaluated TGFβ3 protein levels in extracellular vesicles (EVs) released by HNSCC cells as a predictor for response to chemoradiation therapy (CRT). To this end, specific EV-fractions were isolated from cell lines or HNSCC patient plasma, and TGFβ3 protein was quantified. In patients treated with CRT, TGFβ3 levels were found to be significantly higher in plasma EV-fractions or non-responders compared with responders. High levels of TGFβ3 levels in Annexin V-EVs were associated with the worst progression-free survival. In vitro experiments demonstrated that TGFβ3 silencing sensitized HNSCC cells to cytotoxic therapies, and this phenotype could be rescued by treatment with exogenous. In addition, specific EV-fractions shed by cisplatin-resistant cells were sufficient to transfer the resistant phenotype to sensitive cells through activation of TGFβ-signaling pathway. Therefore, our data show that TGFβ3 transmitted through EV plays a significant role in response to cytotoxic therapy, which can be exploited as a potential biomarker for CRT response in HNSCC patients treated with curative intent.
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Affiliation(s)
- Dorival Mendes Rodrigues-Junior
- Department of Biological Sciences, Universidade Federal de São Paulo, Diadema, Brazil.,Cancer Therapeutics Research Laboratory, National Cancer Centre of Singapore, Singapore
| | - Soon Sim Tan
- Institute of Medical Biology, A*-STAR, Singapore
| | | | - Hui Sun Leong
- Cancer Therapeutics Research Laboratory, National Cancer Centre of Singapore, Singapore
| | | | | | | | - Daniel S W Tan
- Cancer Therapeutics Research Laboratory, National Cancer Centre of Singapore, Singapore.,Division of Medical Oncology, National Cancer Centre of Singapore, Singapore
| | | | - N Gopalakrishna Iyer
- Cancer Therapeutics Research Laboratory, National Cancer Centre of Singapore, Singapore.,Division of Surgical Oncology, National Cancer Centre of Singapore, Singapore
| | - Andre Luiz Vettore
- Department of Biological Sciences, Universidade Federal de São Paulo, Diadema, Brazil
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