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Bhattacharyya S, Ehsan SF, Karacosta LG. Phenotypic maps for precision medicine: a promising systems biology tool for assessing therapy response and resistance at a personalized level. FRONTIERS IN NETWORK PHYSIOLOGY 2023; 3:1256104. [PMID: 37964768 PMCID: PMC10642209 DOI: 10.3389/fnetp.2023.1256104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/28/2023] [Indexed: 11/16/2023]
Abstract
In this perspective we discuss how tumor heterogeneity and therapy resistance necessitate a focus on more personalized approaches, prompting a shift toward precision medicine. At the heart of the shift towards personalized medicine, omics-driven systems biology becomes a driving force as it leverages high-throughput technologies and novel bioinformatics tools. These enable the creation of systems-based maps, providing a comprehensive view of individual tumor's functional plasticity. We highlight the innovative PHENOSTAMP program, which leverages high-dimensional data to construct a visually intuitive and user-friendly map. This map was created to encapsulate complex transitional states in cancer cells, such as Epithelial-Mesenchymal Transition (EMT) and Mesenchymal-Epithelial Transition (MET), offering a visually intuitive way to understand disease progression and therapeutic responses at single-cell resolution in relation to EMT-related single-cell phenotypes. Most importantly, PHENOSTAMP functions as a reference map, which allows researchers and clinicians to assess one clinical specimen at a time in relation to their phenotypic heterogeneity, setting the foundation on constructing phenotypic maps for personalized medicine. This perspective argues that such dynamic predictive maps could also catalyze the development of personalized cancer treatment. They hold the potential to transform our understanding of cancer biology, providing a foundation for a future where therapy is tailored to each patient's unique molecular and cellular tumor profile. As our knowledge of cancer expands, these maps can be continually refined, ensuring they remain a valuable tool in precision oncology.
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Affiliation(s)
- Sayantan Bhattacharyya
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Shafqat F. Ehsan
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Loukia G. Karacosta
- Department of Cancer Systems Imaging, University of Texas MD Anderson Cancer Center, Houston, TX, United States
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You J, Wang Y, Chen H, Jin F. RIPK2: a promising target for cancer treatment. Front Pharmacol 2023; 14:1192970. [PMID: 37324457 PMCID: PMC10266216 DOI: 10.3389/fphar.2023.1192970] [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: 03/24/2023] [Accepted: 05/18/2023] [Indexed: 06/17/2023] Open
Abstract
As an essential mediator of inflammation and innate immunity, the receptor-interacting serine/threonine-protein kinase-2 (RIPK2) is responsible for transducing signaling downstream of the intracellular peptidoglycan sensors nucleotide oligomerization domain (NOD)-like receptors 1 and 2 (NOD1/2), which will further activate nuclear factor kappa-B (NF-κB) and mitogen-activated protein kinase (MAPK) pathways, leading to the transcription activation of pro-inflammatory cytokines and productive inflammatory response. Thus, the NOD2-RIPK2 signaling pathway has attracted extensive attention due to its significant role in numerous autoimmune diseases, making pharmacologic RIPK2 inhibition a promising strategy, but little is known about its role outside the immune system. Recently, RIPK2 has been related to tumorigenesis and malignant progression for which there is an urgent need for targeted therapies. Herein, we would like to evaluate the feasibility of RIPK2 being the anti-tumor drug target and summarize the research progress of RIPK2 inhibitors. More importantly, following the above contents, we will analyze the possibility of applying small molecule RIPK2 inhibitors to anti-tumor therapy.
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Affiliation(s)
- Jieqiong You
- Shanghai Frontier Health Pharmaceutical Technology Co. Ltd, Shanghai, China
- Shanghai Linnova Pharmaceuticals Co. Ltd, Shanghai, China
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Wang
- Shanghai Frontier Health Pharmaceutical Technology Co. Ltd, Shanghai, China
- Shanghai Linnova Pharmaceuticals Co. Ltd, Shanghai, China
| | - Haifeng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fang Jin
- Shanghai Frontier Health Pharmaceutical Technology Co. Ltd, Shanghai, China
- Shanghai Linnova Pharmaceuticals Co. Ltd, Shanghai, China
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Zhang Z, Yan P, Zhao Y, Ren M, Li Y, Lu G, He S. RIPK2 promotes the progression of colon cancer by regulating BIRC3-mediated ubiquitination of IKBKG. Exp Cell Res 2023; 429:113644. [PMID: 37211186 DOI: 10.1016/j.yexcr.2023.113644] [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: 06/17/2022] [Revised: 05/05/2023] [Accepted: 05/13/2023] [Indexed: 05/23/2023]
Abstract
Colon cancer is a cancer with high morbidity and mortality worldwide. Receptor interacting serine/threonine kinase 2 (RIPK2) has been identified as a proto-oncogene, but its role in colon cancer is largely unknown. Herein, we found that RIPK2 interference could inhibit the proliferation and invasion of colon cancer cells, and promote apoptosis. Baculoviral IAP repeat containing 3 (BIRC3) is an E3 ubiquitin ligase, which was found highly expressed in colon cancer cells. Co-immunoprecipitation (Co-IP) experiments showed that RIPK2 could directly bind with BIRC3. Then, we demonstrated that RIPK2 overexpression promoted the expression of BIRC3, BIRC3 interference could eliminate RIPK2-dependent cell proliferation and invasion, and BIRC3 overexpression rescued the suppressive effect of RIPK2 interference on cell proliferation and invasion. We further identified IKBKG, an inhibitor of nuclear factor kappa B, as a ubiquitination substrate targeted by BIRC3. IKBKG interference could eliminate the inhibitory effect of BIRC3 interference on cell invasion. RIPK2 could promote BIRC3-mediated ubiquitination of IKBKG, inhibit the expression of IKBKG protein, and promote the expression of NF-κB subunits p50 and p65 proteins. In addition, DLD-1 cells transfected with sh-RIPK2 or/and sh-BIRC3 were injected into mice to establish a tumor xenograft model, and we found that administration of sh-RIPK2 or sh-BIRC3 impeded the growth of xenograft tumors in vivo, and co-administration displayed a better inhibitory effect. In general, RIPK2 promotes the progression of colon cancer by promoting BIRC3-mediated ubiquitination of IKBKG and activating the NF-κB signaling pathway.
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Affiliation(s)
- Zhiyong Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi Province, China
| | - Pan Yan
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, And Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, 710032, Shaanxi Province, China
| | - Yan Zhao
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi Province, China
| | - Mudan Ren
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi Province, China
| | - Yarui Li
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi Province, China
| | - Guifang Lu
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi Province, China
| | - Shuixiang He
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi Province, China.
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Mokhtari K, Peymani M, Rashidi M, Hushmandi K, Ghaedi K, Taheriazam A, Hashemi M. Colon cancer transcriptome. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 180-181:49-82. [PMID: 37059270 DOI: 10.1016/j.pbiomolbio.2023.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/16/2023]
Abstract
Over the last four decades, methodological innovations have continuously changed transcriptome profiling. It is now feasible to sequence and quantify the transcriptional outputs of individual cells or thousands of samples using RNA sequencing (RNA-seq). These transcriptomes serve as a connection between cellular behaviors and their underlying molecular mechanisms, such as mutations. This relationship, in the context of cancer, provides a chance to unravel tumor complexity and heterogeneity and uncover novel biomarkers or treatment options. Since colon cancer is one of the most frequent malignancies, its prognosis and diagnosis seem to be critical. The transcriptome technology is developing for an earlier and more accurate diagnosis of cancer which can provide better protectivity and prognostic utility to medical teams and patients. A transcriptome is a whole set of expressed coding and non-coding RNAs in an individual or cell population. The cancer transcriptome includes RNA-based changes. The combined genome and transcriptome of a patient may provide a comprehensive picture of their cancer, and this information is beginning to affect treatment decision-making in real-time. A full assessment of the transcriptome of colon (colorectal) cancer has been assessed in this review paper based on risk factors such as age, obesity, gender, alcohol use, race, and also different stages of cancer, as well as non-coding RNAs like circRNAs, miRNAs, lncRNAs, and siRNAs. Similarly, they have been examined independently in the transcriptome study of colon cancer.
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Affiliation(s)
- Khatere Mokhtari
- Department of Modern Biology, ACECR Institute of Higher Education (Isfahan Branch), Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran; The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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Li QL, Lin X, Yu YL, Chen L, Hu QX, Chen M, Cao N, Zhao C, Wang CY, Huang CW, Li LY, Ye M, Wu M. Genome-wide profiling in colorectal cancer identifies PHF19 and TBC1D16 as oncogenic super enhancers. Nat Commun 2021; 12:6407. [PMID: 34737287 PMCID: PMC8568941 DOI: 10.1038/s41467-021-26600-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 10/15/2021] [Indexed: 11/09/2022] Open
Abstract
Colorectal cancer is one of the most common cancers in the world. Although genomic mutations and single nucleotide polymorphisms have been extensively studied, the epigenomic status in colorectal cancer patient tissues remains elusive. Here, together with genomic and transcriptomic analysis, we use ChIP-Seq to profile active enhancers at the genome wide level in colorectal cancer paired patient tissues (tumor and adjacent tissues from the same patients). In total, we sequence 73 pairs of colorectal cancer tissues and generate 147 H3K27ac ChIP-Seq, 144 RNA-Seq, 147 whole genome sequencing and 86 H3K4me3 ChIP-Seq samples. Our analysis identifies 5590 gain and 1100 lost variant enhancer loci in colorectal cancer, and 334 gain and 121 lost variant super enhancer loci. Multiple key transcription factors in colorectal cancer are predicted with motif analysis and core regulatory circuitry analysis. Further experiments verify the function of the super enhancers governing PHF19 and TBC1D16 in regulating colorectal cancer tumorigenesis, and KLF3 is identified as an oncogenic transcription factor in colorectal cancer. Taken together, our work provides an important epigenomic resource and functional factors for epigenetic studies in colorectal cancer.
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Affiliation(s)
- Qing-Lan Li
- Frontier Science Center for Immunology and Metabolism, RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Intestinal and Colorectal Diseases, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Xiang Lin
- Frontier Science Center for Immunology and Metabolism, RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Intestinal and Colorectal Diseases, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Ya-Li Yu
- Division of Gastroenterology, Department of Geriatrics, Hubei Clinical Centre & Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430072, China
| | - Lin Chen
- Frontier Science Center for Immunology and Metabolism, RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Intestinal and Colorectal Diseases, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Qi-Xin Hu
- Frontier Science Center for Immunology and Metabolism, RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Intestinal and Colorectal Diseases, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Meng Chen
- Division of Gastroenterology, Department of Geriatrics, Hubei Clinical Centre & Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430072, China
| | - Nan Cao
- Division of Gastroenterology, Department of Geriatrics, Hubei Clinical Centre & Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430072, China
| | - Chen Zhao
- Frontier Science Center for Immunology and Metabolism, RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Intestinal and Colorectal Diseases, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Chen-Yu Wang
- Frontier Science Center for Immunology and Metabolism, RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Intestinal and Colorectal Diseases, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Cheng-Wei Huang
- Frontier Science Center for Immunology and Metabolism, RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Intestinal and Colorectal Diseases, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Lian-Yun Li
- Frontier Science Center for Immunology and Metabolism, RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Intestinal and Colorectal Diseases, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Mei Ye
- Division of Gastroenterology, Department of Geriatrics, Hubei Clinical Centre & Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430072, China.
| | - Min Wu
- Frontier Science Center for Immunology and Metabolism, RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Hubei Key Laboratory of Developmentally Originated Disease, Hubei Key Laboratory of Intestinal and Colorectal Diseases, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China.
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Qin Y, Chen L, Chen L. Identification and verification of key cancer genes associated with prognosis of colorectal cancer based on bioinformatics analysis. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2021; 46:1063-1070. [PMID: 34911835 PMCID: PMC10930233 DOI: 10.11817/j.issn.1672-7347.2021.200952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Indexed: 11/03/2022]
Abstract
OBJECTIVES The biomarkers targeting colorectal cancer (CRC) prognosis are short of high accuracy and sensitivity in clinic. Through bioinformatics analysis, we aim to identify and confirm a series of key genes referred to the diagnosis and prognosis of CRC. METHODS GSE31905, GSE35279, and GSE41657 were selected as complete RNA sequencing data sets of CRC and colorectal mucosa (CRM) tissues from the NCBI-GEO database, and the differentially expressed genes (DEGs) were analyzed. The common DEGs in these 3 data sets were obtained by Venn map, and enriched by STRING network system and Cytoscape software. The Kaplan-Meier plotter website was used to verify the correlation between the enriched genes and the prognosis of CRC. RESULTS For the whole RNA sequencing data sets of CRC and normal intestinal mucosa samples, the DEGs of CRC and CRM in the 3 data sets (|log2FC|>2 and P<0.05) were screened by GEO2R tool in NCBI-GEO database. By using Venn graph analysis software, the intersection of up-regulated/down-regulated genes in 3 GSE datasets was obtained, and a total 105 up-regulated genes and 140 down-regulated genes were found in the 3 samples. The up-regulated/down-regulated genes were introduced into the STRING network system to obtain the interacting genes. The interacting gene sets were introduced into Cytoscape software, and 61 up-regulated genes were found by Molecular Complex Detection (MCODE) plug-in. Through the Kaplan-Meier plotter website, we found that EPHB2, KLK8, DIAPH3, STC2, OXTR, MMP7, MET, KRT85, KRT6B, KRT23, and KLK10 genes were highly expressed in CRC, and were related to the prognosis. CONCLUSIONS The above 11 genes verified by bioinformatics retrieval and analysis can predict the poor prognosis of CRC to a certain extent, and they provide a possible target for the diagnosis and treatment of CRC.
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Affiliation(s)
- Yi Qin
- Xiangya School of Public Health, Central South University, Changsha 410078.
| | - Lu Chen
- Department of Gastrointestinal Surgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Lizhang Chen
- Xiangya School of Public Health, Central South University, Changsha 410078.
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Xiang L, Zeng Q, Liu J, Xiao M, He D, Zhang Q, Xie D, Deng M, Zhu Y, Liu Y, Bo H, Liu X, Zhou M, Xiong W, Zhou Y, Zhou J, Li X, Cao K. MAFG-AS1/MAFG positive feedback loop contributes to cisplatin resistance in bladder urothelial carcinoma through antagonistic ferroptosis. Sci Bull (Beijing) 2021; 66:1773-1788. [PMID: 36654385 DOI: 10.1016/j.scib.2021.01.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/25/2020] [Accepted: 01/18/2021] [Indexed: 02/03/2023]
Abstract
Though promoting ferroptosis can reduce cisplatin resistance in tumor cells, ferroptosis and cisplatin resistance in bladder urothelial carcinoma (BUC) following long non-coding RNAs (lncRNAs) is largely unknown. Here, we found the highly expressed lncRNA MAF transcription factor G antisense RNA 1 (MAFG-AS1) in BUC, and its inhibition increased the sensitivity of BUC cells to cisplatin by promoting ferroptosis. Mechanically, binding to iron chaperone poly(rC)-binding protein 2 (PCBP2) facilitated the recruitments of MAFG-AS1 to deubiquitinase ubiquitin carboxyl-terminal hydrolase isozyme L5 (UCHL5), thus stabilizing PCBP2 protein itself. Then PCBP2 was confirmed to interact with ferroportin 1 (FPN1), an iron export protein, leading to inhibition of ferroptosis. Moreover, the expression of MAFG-AS1 was regulated by the transcriptional factor MAFG. Interestingly, MAFG-AS1 stimulated MAFG transcription by recruiting histone acetyltransferase p300 (EP300) to promote the histone 3 at lysine 27 (H3K27ac) at genomic locus of MAFG, forming a MAFG-AS1/MAFG positive feedback loop. In patient samples, higher expression of MAFG-AS1 and MAFG in BUC tissues was significantly correlated with T status and N status, such that MAFG-AS1, MAFG, and the combination of the two were independent prognostic indicators and chemotherapy sensitivity predictive biomarkers for BUC patients. These findings suggest that inhibition of MAFG-AS1 and MAFG can increase the sensitivity of BUC cells to cisplatin through promoting ferroptosis, indicating the novel chemotherapy sensitivity biomarkers and therapeutic target for BUC.
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Affiliation(s)
- Liang Xiang
- Department of Oncology, Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Qinghai Zeng
- Department of Dermatology, Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Jianye Liu
- Department of Urology, Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Mengqing Xiao
- Department of Oncology, Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Dong He
- Department of Respiratory, The Second People's Hospital of Hunan Province, Changsha 410007, China
| | - Qun Zhang
- Department of Radiotherapy, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Dan Xie
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Minhua Deng
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Yuxing Zhu
- Department of Oncology, Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Yan Liu
- Department of Plastic Surgery, Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Hao Bo
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha 410083, China
| | - Xiaoming Liu
- Department of Gastroenterology, Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Ming Zhou
- Cancer Research Institute and Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Central South University, Changsha 410078, China
| | - Wei Xiong
- Cancer Research Institute and Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Central South University, Changsha 410078, China
| | - Yanhong Zhou
- Cancer Research Institute and Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, Central South University, Changsha 410078, China
| | - Jianda Zhou
- Department of Plastic Surgery, Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Xiaohui Li
- Hunan Key Laboratory for Bioanalysis of Complex Matrix Samples, Changsha 410205, China; Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
| | - Ke Cao
- Department of Oncology, Third Xiangya Hospital of Central South University, Changsha 410013, China.
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Jaafar RF, Ibrahim Z, Ataya K, Hassanieh J, Ard N, Faraj W. Receptor-Interacting Serine/Threonine-Protein Kinase-2 as a Potential Prognostic Factor in Colorectal Cancer. ACTA ACUST UNITED AC 2021; 57:medicina57070709. [PMID: 34356990 PMCID: PMC8303330 DOI: 10.3390/medicina57070709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/25/2021] [Accepted: 06/03/2021] [Indexed: 12/24/2022]
Abstract
Background and objectives: Receptor-interacting serine/threonine-protein kinase-2 (RIPK2) is an important mediator in different pathways in the immune and inflammatory response system. RIPK2 was also shown to play different roles in different cancer types; however, in colorectal cancer (CRC), its role is not well established. This study aims at identifying the role of RIPK2 in CRC progression and survival. Materials and methods: Data of patients and mRNA protein expression level of genes associated with CRC (RIPK2, tumor necrosis factor (TNF), TRAF1, TRAF7, KLF6, interlukin-6 (Il6), interlukin-8 (Il8), vascular-endothelial growth factor A (VEGFA), MKI67, TP53, nuclear factor-kappa B (NFKB), NFKB2, BCL2, XIAP, and RELA) were downloaded from the PrognoScan online public database. Patients were divided between low and high RIPK2 expression and different CRC characteristics were studied between the two groups. Survival curves were evaluated using a Kaplan-Meier estimator. The Pearson correlation was used to study the correlation between RIPK2 and the other factors. Statistical analysis was carried out using SPSS version 25.0. The Human Protein Atlas was also used for the relationship between RIPK2 expression in CRC tissues and survival. Differences were considered statistically significant at p < 0.05. Results: A total of 520 patients were downloaded from the PrognoScan database, and RIPK2 was found to correlate with MKI67, TRAF1, KLF6, TNF, Il6, Il8, VEGFA, NFKB2, BCL2, and RELA. High expression of RIPK2 was associated with high expression of VEGFA (p < 0.01) and increased mortality (p < 0.01). Conclusions: In this study, RIPK2 is shown to be a potential prognostic factor in CRC; however, more studies are needed to assess and verify its potential role as a prognostic marker and in targeted therapy.
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Affiliation(s)
- Rola F. Jaafar
- Department of Surgery, American University of Beirut Medical Center, Beirut 1107 2020, Lebanon; (R.F.J.); (Z.I.); (J.H.)
| | - Zeid Ibrahim
- Department of Surgery, American University of Beirut Medical Center, Beirut 1107 2020, Lebanon; (R.F.J.); (Z.I.); (J.H.)
| | - Karim Ataya
- Division of Liver Transplantation, Hepatobiliary and Pancreatic Surgery, Department of General Surgery, American University of Beirut Medical Centre, Beirut 1107 2020, Lebanon;
| | - Joelle Hassanieh
- Department of Surgery, American University of Beirut Medical Center, Beirut 1107 2020, Lebanon; (R.F.J.); (Z.I.); (J.H.)
| | - Natasha Ard
- Department of General Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut 1107 2020, Lebanon;
| | - Walid Faraj
- Department of Surgery, American University of Beirut Medical Center, Beirut 1107 2020, Lebanon; (R.F.J.); (Z.I.); (J.H.)
- Division of Liver Transplantation, Hepatobiliary and Pancreatic Surgery, Department of General Surgery, American University of Beirut Medical Centre, Beirut 1107 2020, Lebanon;
- Correspondence: ; Tel.: +961-350-000 (ext. 5714)
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Screening of immunosuppressive cells from colorectal adenocarcinoma and identification of prognostic markers. Biosci Rep 2021; 41:228002. [PMID: 33646276 PMCID: PMC8024875 DOI: 10.1042/bsr20203496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 02/19/2021] [Accepted: 02/24/2021] [Indexed: 01/08/2023] Open
Abstract
Background: Colorectal cancer (CRC) is the most common type of gastrointestinal malignant tumour. Colorectal adenocarcinoma (COAD) – the most common type of CRC – is particularly dangerous. The role of the immune system in the development of tumour-associated inflammation and cancer has received increasing attention recently. Methods: In the present study, we compiled the expression profiles of 262 patients with complete follow-up data from The Cancer Genome Atlas (TCGA) database as an experimental group and selected 65 samples from the Gene Expression Omnibus (GEO) dataset (of which 46 samples were with M0) as a verification group. First, we screened the immune T helper 17 (Th17) cells related to the prognosis of COAD. Subsequently, we identified Th17 cells-related hub genes by utilising Weighted Gene Co-expression Network Analysis (WGCNA) and Least Absolute Shrinkage and Selector Operation (LASSO) regression analysis. Six genes associated with the prognosis in patients with COAD were identified, including: KRT23, ULBP2, ASRGL1, SERPINA1, SCIN, and SLC28A2. We constructed a clinical prediction model and analysed its predictive power. Results: The identified hub genes are involved in developing many diseases and closely linked to digestive disorders. Our results suggested that the hub genes could influence the prognosis of COAD by regulating Th17 cells’ infiltration. Conclusions: These newly discovered hub genes contribute to clarifying the mechanisms of COAD development and metastasis. Given that they promote COAD development, they may become new therapeutic targets and biomarkers of COAD.
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Wüst HM, Wegener A, Fröb F, Hartwig AC, Wegwitz F, Kari V, Schimmel M, Tamm ER, Johnsen SA, Wegner M, Sock E. Egr2-guided histone H2B monoubiquitination is required for peripheral nervous system myelination. Nucleic Acids Res 2020; 48:8959-8976. [PMID: 32672815 PMCID: PMC7498331 DOI: 10.1093/nar/gkaa606] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 12/30/2022] Open
Abstract
Schwann cells are the nerve ensheathing cells of the peripheral nervous system. Absence, loss and malfunction of Schwann cells or their myelin sheaths lead to peripheral neuropathies such as Charcot-Marie-Tooth disease in humans. During Schwann cell development and myelination chromatin is dramatically modified. However, impact and functional relevance of these modifications are poorly understood. Here, we analyzed histone H2B monoubiquitination as one such chromatin modification by conditionally deleting the Rnf40 subunit of the responsible E3 ligase in mice. Rnf40-deficient Schwann cells were arrested immediately before myelination or generated abnormally thin, unstable myelin, resulting in a peripheral neuropathy characterized by hypomyelination and progressive axonal degeneration. By combining sequencing techniques with functional studies we show that H2B monoubiquitination does not influence global gene expression patterns, but instead ensures selective high expression of myelin and lipid biosynthesis genes and proper repression of immaturity genes. This requires the specific recruitment of the Rnf40-containing E3 ligase by Egr2, the central transcriptional regulator of peripheral myelination, to its target genes. Our study identifies histone ubiquitination as essential for Schwann cell myelination and unravels new disease-relevant links between chromatin modifications and transcription factors in the underlying regulatory network.
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Affiliation(s)
- Hannah M Wüst
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstrasse 17, D-91054 Erlangen, Germany
| | - Amélie Wegener
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstrasse 17, D-91054 Erlangen, Germany
| | - Franziska Fröb
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstrasse 17, D-91054 Erlangen, Germany
| | - Anna C Hartwig
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstrasse 17, D-91054 Erlangen, Germany
| | - Florian Wegwitz
- Department of General, Visceral, and Pediatric Surgery, University Medical Center Göttingen, D-37075 Göttingen, Germany
| | - Vijayalakshmi Kari
- Department of General, Visceral, and Pediatric Surgery, University Medical Center Göttingen, D-37075 Göttingen, Germany
| | - Margit Schimmel
- Institut für Humananatomie und Embryologie, Universität Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
| | - Ernst R Tamm
- Institut für Humananatomie und Embryologie, Universität Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
| | - Steven A Johnsen
- Department of General, Visceral, and Pediatric Surgery, University Medical Center Göttingen, D-37075 Göttingen, Germany.,Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN, USA
| | - Michael Wegner
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstrasse 17, D-91054 Erlangen, Germany
| | - Elisabeth Sock
- Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstrasse 17, D-91054 Erlangen, Germany
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