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Fan Z, Edelmann D, Yuan T, Köhler BC, Hoffmeister M, Brenner H. Developing survival prediction models in colorectal cancer using epigenome-wide DNA methylation data from whole blood. NPJ Precis Oncol 2024; 8:191. [PMID: 39237753 PMCID: PMC11377733 DOI: 10.1038/s41698-024-00689-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 08/28/2024] [Indexed: 09/07/2024] Open
Abstract
While genome-wide association studies are valuable in identifying CRC survival predictors, the benefit of adding blood DNA methylation (blood-DNAm) to clinical features, including the TNM system, remains unclear. In a multi-site population-based patient cohort study of 2116 CRC patients with baseline blood-DNAm, we analyzed survival predictions using eXtreme Gradient Boosting with a 5-fold nested leave-sites-out cross-validation across four groups: traditional and comprehensive clinical features, blood-DNAm, and their combination. Model performance was assessed using time-dependent ROC curves and calibrations. During a median follow-up of 10.3 years, 1166 patients died. Although blood-DNAm-based predictive signatures achieved moderate performances, predictive signatures based on clinical features outperformed blood-DNAm signatures. The inclusion of blood-DNAm did not improve survival prediction over clinical features. M1 stage, age at blood collection, and N2 stage were the top contributors. Despite some prognostic value, incorporating blood DNA methylation did not enhance survival prediction of CRC patients beyond clinical features.
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Affiliation(s)
- Ziwen Fan
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominic Edelmann
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tanwei Yuan
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bruno Christian Köhler
- Liver Cancer Center Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- NCT Heidelberg, National Center for Tumor Diseases (NCT) a partnership between DKFZ and University Hospital, Heidelberg, Germany.
- Division of Preventive Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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2
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Tian S, Zhong K, Yang Z, Fu J, Cai Y, Xiao M. Investigating the mechanism of tricyclic decyl benzoxazole -induced apoptosis in liver Cancer cells through p300-mediated FOXO3 activation. Cell Signal 2024; 121:111280. [PMID: 38960058 DOI: 10.1016/j.cellsig.2024.111280] [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] [Received: 04/10/2024] [Revised: 06/07/2024] [Accepted: 06/26/2024] [Indexed: 07/05/2024]
Abstract
OBJECTIVE To investigate whether tricyclic decylbenzoxazole (TDB) regulates liver cancer cell proliferation and apoptosis through p300-mediated FOXO acetylation. METHODS Sequencing, adenovirus, and lentivirus transfection were performed in human liver cancer cell line SMMC-7721 and apoptosis was detected by Tunel, Hoechst, and flow cytometry. TEM for mitochondrial morphology, MTT for cell proliferation ability, Western blot, and PCR were used to detect protein levels and mRNA changes. RESULTS Sequencing analysis and cell experiments confirmed that TDB can promote the up-regulation of FOXO3 expression. TDB induced FOXO3 up-regulation in a dose-dependent manner, promoted the expression of p300 and Bim, and enhanced the acetylation and dephosphorylation of FOXO3, thus promoting apoptosis. p300 promotes apoptosis of cancer cells through Bim and other proteins, while HAT enhances the phosphorylation of FOXO3 and inhibits apoptosis. Overexpression of FOXO3 can increase the expression of exo-apoptotic pathways (FasL, TRAIL), endo-apoptotic pathways (Bim), and acetylation at the protein level and inhibit cell proliferation and apoptotic ability, while FOXO3 silencing or p300 mutation can partially reverse apoptosis. In tumor tissues with overexpression of FOXO3, TDB intervention can further increase the expression of p53 and caspase-9 proteins in tumor cells, resulting in loss of mitochondrial membrane integrity during apoptosis, the release of cytoplasm during signal transduction, activation of caspase-9 and synergistic inhibition of growth. CONCLUSION TDB induces proliferation inhibition and promotes apoptosis of SMMC-7721 cells by activating p300-mediated FOXO3 acetylation.
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Affiliation(s)
- Shuhong Tian
- Research Center for Drug Safety Evaluation of Hainan Province, Hainan Medical University, Haikou 571199, China
| | - Keyan Zhong
- Clinical Skills Experimental Teaching Center of Hainan Medical University, Haikou 571199, China
| | - Zhaoxin Yang
- Research Center for Drug Safety Evaluation of Hainan Province, Hainan Medical University, Haikou 571199, China
| | - Jian Fu
- Research Center for Drug Safety Evaluation of Hainan Province, Hainan Medical University, Haikou 571199, China
| | - Yangbo Cai
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Hainan Medical University, Haikou 570100, China
| | - Min Xiao
- Research Center for Drug Safety Evaluation of Hainan Province, Hainan Medical University, Haikou 571199, China.
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Nandwa JO, Mehmood A, Mahjabeen I, Raheem KY, Hamadou M, Raimi MZ, Kayani MA. miR-4716-3p and the target AKT2 Gene/rs2304186 SNP are associated with blood cancer pathogenesis in Pakistani population. Noncoding RNA Res 2024; 9:695-703. [PMID: 38577021 PMCID: PMC10990746 DOI: 10.1016/j.ncrna.2024.03.005] [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: 01/25/2024] [Revised: 02/28/2024] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
AKT2 is crucial for cancer cells' invasion, metastasis, and survival. It is a possible downstream gene target of cancer glycolysis-related microRNAs. The study investigated the role of miRNA-4716-3p, rs2304186, and the AKT2 gene in blood cancer pathogenesis. RT-qPCR was used to analyze AKT2 gene mRNA and miRNA-4716-3p expression in 200 blood cancer samples and 200 healthy controls. Furthermore, Tetra-ARMS PCR was used to examine the rs2304186 AKT2 SNP in 300 patients and 290 control samples. miRNA-4716-3p was shown to be significantly downregulated (p = 0.0294), whereas mRNA expression of the AKT2 gene was found to be significantly upregulated (p = 0.0034) in blood cancer patients compared to healthy individuals. miRNA-4716-3p downregulation (p = 0.0466) was more pronounced, while AKT2 upregulation was non-significant (p = 0.1661) in untreated patients compared to chemotherapy-treated patients. Blood cancer risk was significantly associated with the rs2304186 GT genotype (p = 0.0432), TT genotype (p = 0.0502), and mutant allele (T) frequency (p = 0.0008). Polymorphism rs2304186 was associated with an increased risk of blood cancer in dominant (p = 0.0011), recessive (p = 0.0502), and additive (p = 0.0008) genetic models. The results suggested that the rs2304186 and the deregulated expression of miRNA-4716-3p and AKT2 gene at the mRNA level may significantly increase the incidence of blood cancer, particularly in the Pakistani population. Therefore, these may function as suitable biomarkers for blood cancer diagnosis and prognosis. Additional, larger-scale investigations may be required to affirm these results.
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Affiliation(s)
- Jairus Olumasai Nandwa
- Department of Biosciences, COMSATS University Islamabad, Pakistan
- Department of Public Needs Research, Integrated Cancer Research Foundation of Kenya, Kenya
- Department of Genetics, Hebrew University of Jerusalem, Israel
| | - Azhar Mehmood
- Department of Biosciences, COMSATS University Islamabad, Pakistan
| | - Ishrat Mahjabeen
- Department of Biosciences, COMSATS University Islamabad, Pakistan
| | | | - Mamoudou Hamadou
- Department of Biological Sciences, Faculty of Science, University of Maroua, Cameroon
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4
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Herrera-Orozco H, García-Castillo V, López-Urrutia E, Martinez-Gutierrez AD, Pérez-Yepez E, Millán-Catalán O, Cantú de León D, López-Camarillo C, Jacobo-Herrera NJ, Rodríguez-Dorantes M, Ramos-Payán R, Pérez-Plasencia C. Somatic Copy Number Alterations in Colorectal Cancer Lead to a Differentially Expressed ceRNA Network (ceRNet). Curr Issues Mol Biol 2023; 45:9549-9565. [PMID: 38132443 PMCID: PMC10742218 DOI: 10.3390/cimb45120597] [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: 10/20/2023] [Revised: 11/14/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Colorectal cancer (CRC) represents the second deadliest malignancy worldwide. Around 75% of CRC patients exhibit high levels of chromosome instability that result in the accumulation of somatic copy number alterations. These alterations are associated with the amplification of oncogenes and deletion of tumor-ppressor genes and contribute to the tumoral phenotype in different malignancies. Even though this relationship is well known, much remains to be investigated regarding the effect of said alterations in long non-coding RNAs (lncRNAs) and, in turn, the impact these alterations have on the tumor phenotype. The present study aimed to evaluate the role of differentially expressed lncRNAs coded in regions with copy number alterations in colorectal cancer patient samples. We downloaded RNA-seq files of the Colorectal Adenocarcinoma Project from the The Cancer Genome Atlas (TCGA) repository (285 sequenced tumor tissues and 41 non-tumor tissues), evaluated differential expression, and mapped them over genome sequencing data with regions presenting copy number alterations. We obtained 78 differentially expressed (LFC > 1|< -1, padj < 0.05) lncRNAs, 410 miRNAs, and 5028 mRNAs and constructed a competing endogenous RNA (ceRNA) network, predicting significant lncRNA-miRNA-mRNA interactions. Said network consisted of 30 lncRNAs, 19 miRNAs, and 77 mRNAs. To understand the role that our ceRNA network played, we performed KEGG and GO analysis and found several oncogenic and anti-oncogenic processes enriched by the molecular players in our network. Finally, to evaluate the clinical relevance of the lncRNA expression, we performed survival analysis and found that C5orf64, HOTAIR, and RRN3P3 correlated with overall patient survival. Our results showed that lncRNAs coded in regions affected by SCNAs form a complex gene regulatory network in CCR.
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Affiliation(s)
- Héctor Herrera-Orozco
- Laboratorio de Genómica, FES-Iztacala, Universidad Nacional Autónoma de México. Av. De los Barrios 1, Los Reyes Iztacala, Tlalnepantla 54090, Mexico; (H.H.-O.); (V.G.-C.); (E.L.-U.)
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Edificio D. Circuito de Posgrados, Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico
| | - Verónica García-Castillo
- Laboratorio de Genómica, FES-Iztacala, Universidad Nacional Autónoma de México. Av. De los Barrios 1, Los Reyes Iztacala, Tlalnepantla 54090, Mexico; (H.H.-O.); (V.G.-C.); (E.L.-U.)
| | - Eduardo López-Urrutia
- Laboratorio de Genómica, FES-Iztacala, Universidad Nacional Autónoma de México. Av. De los Barrios 1, Los Reyes Iztacala, Tlalnepantla 54090, Mexico; (H.H.-O.); (V.G.-C.); (E.L.-U.)
| | - Antonio Daniel Martinez-Gutierrez
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Tlalpan, Mexico City 14080, Mexico; (A.D.M.-G.); (E.P.-Y.); (O.M.-C.); (D.C.d.L.)
| | - Eloy Pérez-Yepez
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Tlalpan, Mexico City 14080, Mexico; (A.D.M.-G.); (E.P.-Y.); (O.M.-C.); (D.C.d.L.)
| | - Oliver Millán-Catalán
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Tlalpan, Mexico City 14080, Mexico; (A.D.M.-G.); (E.P.-Y.); (O.M.-C.); (D.C.d.L.)
| | - David Cantú de León
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Tlalpan, Mexico City 14080, Mexico; (A.D.M.-G.); (E.P.-Y.); (O.M.-C.); (D.C.d.L.)
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Calle Dr. García Diego 168, Cuauhtémoc, Mexico City 06720, Mexico;
| | - Nadia J. Jacobo-Herrera
- Unidad de Bioquímica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Av. Vasco de Quiroga 15, Tlalpan, Mexico City 14080, Mexico;
| | | | - Rosalío Ramos-Payán
- Faculty of Chemical and Biological Sciences, Autonomous University of Sinaloa, Culiacan 80030, Mexico;
| | - Carlos Pérez-Plasencia
- Laboratorio de Genómica, FES-Iztacala, Universidad Nacional Autónoma de México. Av. De los Barrios 1, Los Reyes Iztacala, Tlalnepantla 54090, Mexico; (H.H.-O.); (V.G.-C.); (E.L.-U.)
- Laboratorio de Genómica, Instituto Nacional de Cancerología, Av. San Fernando 22, Tlalpan, Mexico City 14080, Mexico; (A.D.M.-G.); (E.P.-Y.); (O.M.-C.); (D.C.d.L.)
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Kiełbowski K, Ptaszyński K, Wójcik J, Wojtyś ME. The role of selected non-coding RNAs in the biology of non-small cell lung cancer. Adv Med Sci 2023; 68:121-137. [PMID: 36933328 DOI: 10.1016/j.advms.2023.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/26/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023]
Abstract
Lung cancer is the second most frequently diagnosed cancer worldwide and a leading cause of cancer-related deaths. Non-small cell lung carcinoma (NSCLC) represents 85% of all cases. Accumulating evidence highlights the outstanding role of non-coding RNA (ncRNA) in regulating the tumorigenesis process by modulating crucial signaling pathways. Micro RNA (miRNA), long non-coding RNA (lncRNA) and circular RNA (circRNA) are either up- or downregulated in lung cancer patients and can promote or suppress the progression of the disease. These molecules interact with messenger RNA (mRNA) and with each other to regulate gene expression and stimulate proto-oncogenes or silence tumor suppressors. NcRNAs provide a new strategy to diagnose or treat lung cancer patients and multiple molecules have already been identified as potential biomarkers or therapeutic targets. The aim of this review is to summarize the current evidence on the roles of miRNA, lncRNA and circRNA in NSCLC biology and present their clinical potential.
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Affiliation(s)
- Kajetan Kiełbowski
- Department of Thoracic Surgery and Transplantation, Pomeranian Medical University, Szczecin, Poland
| | - Konrad Ptaszyński
- Department of Pathology, Faculty of Medicine, Collegium Medicum, University of Warmia and Mazury in Olsztyn, Poland
| | - Janusz Wójcik
- Department of Thoracic Surgery and Transplantation, Pomeranian Medical University, Szczecin, Poland
| | - Małgorzata Edyta Wojtyś
- Department of Thoracic Surgery and Transplantation, Pomeranian Medical University, Szczecin, Poland.
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6
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Blood-based DNA methylation signatures in cancer: A systematic review. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166583. [PMID: 36270476 DOI: 10.1016/j.bbadis.2022.166583] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022]
Abstract
DNA methylation profiles are in dynamic equilibrium via the initiation of methylation, maintenance of methylation and demethylation, which control gene expression and chromosome stability. Changes in DNA methylation patterns play important roles in carcinogenesis and primarily manifests as hypomethylation of the entire genome and the hypermethylation of individual loci. These changes may be reflected in blood-based DNA, which provides a non-invasive means for cancer monitoring. Previous blood-based DNA detection objects primarily included circulating tumor DNA/cell-free DNA (ctDNA/cfDNA), circulating tumor cells (CTCs) and exosomes. Researchers gradually found that methylation changes in peripheral blood mononuclear cells (PBMCs) also reflected the presence of tumors. Blood-based DNA methylation is widely used in early diagnosis, prognosis prediction, dynamic monitoring after treatment and other fields of clinical research on cancer. The reversible methylation of genes also makes them important therapeutic targets. The present paper summarizes the changes in DNA methylation in cancer based on existing research and focuses on the characteristics of the detection objects of blood-based DNA, including ctDNA/cfDNA, CTCs, exosomes and PBMCs, and their application in clinical research.
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7
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Xie J, Zhang J, Tian W, Zou Y, Tang Y, Zheng S, Wong CW, Deng X, Wu S, Chen J, Mo Y, Xie X. The Pan-Cancer Multi-Omics Landscape of FOXO Family Relevant to Clinical Outcome and Drug Resistance. Int J Mol Sci 2022; 23:ijms232415647. [PMID: 36555288 PMCID: PMC9778770 DOI: 10.3390/ijms232415647] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
The forkhead box O (FOXO) transcription factors (TFs) family are frequently mutated, deleted, or amplified in various human cancers, making them attractive candidates for therapy. However, their roles in pan-cancer remain unclear. Here, we evaluated the expression, prognostic value, mutation, methylation, and clinical features of four FOXO family genes (FOXO1, FOXO3, FOXO4, and FOXO6) in 33 types of cancers based on the Cancer Genome Atlas (TCGA) and Genotype Tissue Expression (GTEx) databases. We used a single sample gene set enrichment analysis (ssGSEA) algorithm to establish a novel index called "FOXOs score". Moreover, we investigated the association between the FOXOs score and tumor microenvironment (TME), the responses to multiple treatments, along with drug resistance. We found that the FOXO family genes participated in tumor progression and were related to the prognosis in various types of cancer. We calculated the FOXOs score and found that it was significantly correlated with multiple malignant pathways in pan-cancer, including Wnt/beta-catenin signaling, TGF-beta signaling, and hedgehog signaling. In addition, the FOXOs score was also associated with multiple immune-related characteristics. Furthermore, the FOXOs score was sensitive for predicting the efficacy of diverse treatments in multiple cancers, especially immunotherapy. In conclusion, FOXO family genes were vital in pan-cancer and were strongly correlated with the TME. A high FOXOs score indicated an excellent immune-activated TME and sensitivity to multiple treatments. Hence, the FOXOs score might potentially be used as a biomarker in patients with a tumor.
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Affiliation(s)
- Jindong Xie
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Junsheng Zhang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Wenwen Tian
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Yutian Zou
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Yuhui Tang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Shaoquan Zheng
- Breast Disease Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510060, China
| | - Chau-Wei Wong
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Xinpei Deng
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Song Wu
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Junxin Chen
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510060, China
| | - Yunxian Mo
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Correspondence: (Y.M.); (X.X.); Tel.: +86-13924277788 (X.X.); Fax: +86-20-87343805 (X.X.)
| | - Xiaoming Xie
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Correspondence: (Y.M.); (X.X.); Tel.: +86-13924277788 (X.X.); Fax: +86-20-87343805 (X.X.)
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Chen Z, Mei K, Xiao Y, Xiong Y, Long W, Wang Q, Zhong J, Di D, Ge Y, Luo Y, Li Z, Huang Y, Gu R, Wang B. Prognostic Assessment of Oxidative Stress-Related Genes in Colorectal Cancer and New Insights into Tumor Immunity. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:2518340. [PMID: 36299603 PMCID: PMC9590115 DOI: 10.1155/2022/2518340] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/21/2022] [Indexed: 11/19/2022]
Abstract
Oxidative stress is crucial to the biology of tumors. Oxidative stress' potential predictive significance in colorectal cancer (CRC) has not been studied; nevertheless here, we developed a forecasting model based on oxidative stress to forecast the result of CRC survival and enhance clinical judgment. The training set was chosen from the transcriptomes of 177 CRC patients in GSE17536. For validation, 65 samples of colon cancer from GSE29621 were utilized. For the purpose of choosing prognostic genes, the expression of oxidative stress-related genes (OXEGs) was found. Prognostic risk models were built using multivariate Cox regression analysis, univariate Cox regression analysis, and LASSO regression analysis. The outcomes of the western blot and transcriptome sequencing tests were finally confirmed. ATF4, CARS2, CRP, GPX1, IL1B, MAPK8, MRPL44, MTFMT, NOS1, OSGIN2, SOD2, AARS2, and FOXO3 were among the 14 OXEGs used to build prognostic characteristics. Patients with CRC were categorized into low-risk and high-risk groups according on their median risk scores. Cox regression analysis using single and multiple variables revealed that OXEG-related signals were independent risk factors for CRC. Additionally, the validation outcomes from western blotting and transcriptome sequencing demonstrated that OXEGs were differently expressed. Using 14 OXEGs, our work creates a predictive signature that may be applied to the creation of new prognostic models and the identification of possible medication candidates for the treatment of CRC.
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Affiliation(s)
- Zilu Chen
- Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Kun Mei
- Department of Cardiothoracic Surgery, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China
| | - Yao Xiao
- Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yan Xiong
- Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Wei Long
- Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Qin Wang
- Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jiang Zhong
- Department of Ultrasound, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing 210001, China
| | - Dongmei Di
- Department of Cardiothoracic Surgery, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China
| | - Yunxi Ge
- Department of Ultrasound, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing 210001, China
| | - Yi Luo
- Department of Oncology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210028, China
- Department of Oncology, Jiangsu Province Hospital on Integration of Chinese and Western Medicine, Nanjing, Jiangsu 210028, China
| | - Ziyun Li
- Nanjing University of Chinese Medicine, Nanjing 210023, China
- School of Acupuncture and Tuina, School of Regimen and Rehabilitation, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yan Huang
- Department of Ultrasound, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing 210001, China
| | - Renjun Gu
- Nanjing University of Chinese Medicine, Nanjing 210023, China
- School of Chinese Medicine & School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Bin Wang
- Department of Cardiothoracic Surgery, The Third Affiliated Hospital of Soochow University, Changzhou 213003, China
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9
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Gouda MA, Duose DY, Lapin M, Zalles S, Huang HJ, Xi Y, Zheng X, Aldesoky AI, Alhanafy AM, Shehata MA, Wang J, Kopetz S, Meric-Bernstam F, Wistuba II, Luthra R, Janku F. Mutation-Agnostic Detection of Colorectal Cancer Using Liquid Biopsy-Based Methylation-Specific Signatures. Oncologist 2022; 28:368-372. [PMID: 36200910 PMCID: PMC10078907 DOI: 10.1093/oncolo/oyac204] [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: 06/09/2022] [Accepted: 08/29/2022] [Indexed: 11/12/2022] Open
Abstract
Detection of methylation patterns in circulating tumor DNA (ctDNA) can offer a novel approach for cancer diagnostics given the unique signature for each tumor type. We developed a next-generation sequencing (NGS)-based assay targeting 32 CpG sites to detect colorectal cancer-specific ctDNA. NGS was performed on bisulfite-converted libraries and status dichotomization was done using median methylation ratios at all targets. We included plasma samples from patients with metastatic colorectal (n = 20) and non-colorectal cancers (n = 8); and healthy volunteers (n = 4). Median methylation ratio was higher in colorectal cancer compared with non-colorectal cancers (P = .001) and normal donors (P = .005). The assay detected ctDNA in 85% of patients with colorectal cancer at a specificity of 92%. Notably, we were able to detect methylated ctDNA in 75% of patients in whom ctDNA was not detected by other methods. Detection of methylated ctDNA was associated with shorter median progression-free survival compared to non-detection (8 weeks versus 54 weeks; P = .027).
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Affiliation(s)
- Mohamed A Gouda
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA.,Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA.,Department of Clinical Oncology and Nuclear Medicine, Faculty of Medicine, Menoufia University, Shebin Al-Kom, Egypt
| | - Dzifa Y Duose
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Morten Lapin
- Department of Hematology and Oncology, Stavanger University Hospital, Stavanger, Norway
| | - Stephanie Zalles
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Helen J Huang
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Yuanxin Xi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Xiaofeng Zheng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Amira I Aldesoky
- Department of Clinical Oncology and Nuclear Medicine, Faculty of Medicine, Menoufia University, Shebin Al-Kom, Egypt
| | - Alshimaa M Alhanafy
- Department of Clinical Oncology and Nuclear Medicine, Faculty of Medicine, Menoufia University, Shebin Al-Kom, Egypt
| | - Mohamed A Shehata
- Department of Clinical Oncology and Nuclear Medicine, Faculty of Medicine, Menoufia University, Shebin Al-Kom, Egypt
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Rajyalakshmi Luthra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Filip Janku
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
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