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Bhattacharjya A, Islam MM, Uddin MA, Talukder MA, Azad A, Aryal S, Paul BK, Tasnim W, Almoyad MAA, Moni MA. Exploring gene regulatory interaction networks and predicting therapeutic molecules for hypopharyngeal cancer and EGFR-mutated lung adenocarcinoma. FEBS Open Bio 2024. [PMID: 38783639 DOI: 10.1002/2211-5463.13807] [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: 06/24/2023] [Revised: 01/30/2024] [Accepted: 04/16/2024] [Indexed: 05/25/2024] Open
Abstract
Hypopharyngeal cancer gene regulatory networks and therapeutic molecules are a disease that is associated with EGFR-mutated lung adenocarcinoma. Here we utilized a bioinformatics approach to identify genetic commonalities between these two diseases. To this end, we examined microarray datasets from GEO (Gene Expression Omnibus) to identify differentially expressed genes, common genes, and hub genes between the selected two diseases. Our analyses identified potential therapeutic molecules for the selected diseases based on 10 hub genes with the highest interactions according to the degree topology method and the maximum clique centrality (MCC). These therapeutic molecules may have the potential for simultaneous treatment of these diseases.
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Affiliation(s)
- Abanti Bhattacharjya
- Department of Computer Science and Engineering, Jagannath University, Dhaka, Bangladesh
| | - Md Manowarul Islam
- Department of Computer Science and Engineering, Jagannath University, Dhaka, Bangladesh
| | - Md Ashraf Uddin
- School of Information Technology, Deakin University, Geelong, Australia
| | - Md Alamin Talukder
- Department of Computer Science and Engineering, International University of Business Agriculture and Technology, Dhaka, Bangladesh
| | - Akm Azad
- Department of Mathematics and Statistics, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Sunil Aryal
- School of Information Technology, Deakin University, Geelong, Australia
| | - Bikash Kumar Paul
- Department of Information and Communication Technology, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
- Department of Software Engineering, Daffodil International University, Dhaka, Bangladesh
| | - Wahia Tasnim
- Department of Information and Communication Technology, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | | | - Mohammad Ali Moni
- Artificial Intelligence & Data Science, Faculty of Health and Behavioural Sciences, The University of Queensland, Brisbane, Australia
- AI & Digital Health Technology, Artificial Intelligence and Cyber Futures Institute, Charles Sturt University, Bathurst, Australia
- Rural Health Research Institute, Charles Sturt University, Orange, Australia
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Caputo WL, de Souza MC, Basso CR, Pedrosa VDA, Seiva FRF. Comprehensive Profiling and Therapeutic Insights into Differentially Expressed Genes in Hepatocellular Carcinoma. Cancers (Basel) 2023; 15:5653. [PMID: 38067357 PMCID: PMC10705715 DOI: 10.3390/cancers15235653] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/02/2023] [Accepted: 11/04/2023] [Indexed: 02/16/2024] Open
Abstract
Background: Drug repurposing is a strategy that complements the conventional approach of developing new drugs. Hepatocellular carcinoma (HCC) is a highly prevalent type of liver cancer, necessitating an in-depth understanding of the underlying molecular alterations for improved treatment. Methods: We searched for a vast array of microarray experiments in addition to RNA-seq data. Through rigorous filtering processes, we have identified highly representative differentially expressed genes (DEGs) between tumor and non-tumor liver tissues and identified a distinct class of possible new candidate drugs. Results: Functional enrichment analysis revealed distinct biological processes associated with metal ions, including zinc, cadmium, and copper, potentially implicating chronic metal ion exposure in tumorigenesis. Conversely, up-regulated genes are associated with mitotic events and kinase activities, aligning with the relevance of kinases in HCC. To unravel the regulatory networks governing these DEGs, we employed topological analysis methods, identifying 25 hub genes and their regulatory transcription factors. In the pursuit of potential therapeutic options, we explored drug repurposing strategies based on computational approaches, analyzing their potential to reverse the expression patterns of key genes, including AURKA, CCNB1, CDK1, RRM2, and TOP2A. Potential therapeutic chemicals are alvocidib, AT-7519, kenpaullone, PHA-793887, JNJ-7706621, danusertibe, doxorubicin and analogues, mitoxantrone, podofilox, teniposide, and amonafide. Conclusion: This multi-omic study offers a comprehensive view of DEGs in HCC, shedding light on potential therapeutic targets and drug repurposing opportunities.
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Affiliation(s)
- Wesley Ladeira Caputo
- Post Graduation Program in Experimental Pathology, State University of Londrina (UEL), Londrina 86057-970, PR, Brazil; (W.L.C.); (M.C.d.S.)
| | - Milena Cremer de Souza
- Post Graduation Program in Experimental Pathology, State University of Londrina (UEL), Londrina 86057-970, PR, Brazil; (W.L.C.); (M.C.d.S.)
| | - Caroline Rodrigues Basso
- Department of Chemical and Biological Sciences, Institute of Bioscience, São Paulo State University (UNESP), Botucatu 18610-034, SP, Brazil; (C.R.B.); (V.d.A.P.)
| | - Valber de Albuquerque Pedrosa
- Department of Chemical and Biological Sciences, Institute of Bioscience, São Paulo State University (UNESP), Botucatu 18610-034, SP, Brazil; (C.R.B.); (V.d.A.P.)
| | - Fábio Rodrigues Ferreira Seiva
- Post Graduation Program in Experimental Pathology, State University of Londrina (UEL), Londrina 86057-970, PR, Brazil; (W.L.C.); (M.C.d.S.)
- Department of Chemical and Biological Sciences, Institute of Bioscience, São Paulo State University (UNESP), Botucatu 18610-034, SP, Brazil; (C.R.B.); (V.d.A.P.)
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Aba N, Koçpınar EF, Ceylani T. The Hepatic Antioxidant System Damage Induced with the Cafeteria (CAF) Diet Is Largely Counteracted Using SCD Probiotics during Development of Male Wistar Rats. Nutrients 2023; 15:4557. [PMID: 37960210 PMCID: PMC10648500 DOI: 10.3390/nu15214557] [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: 09/30/2023] [Revised: 10/16/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
The cafeteria (CAF) diet, reflective of predominant Western dietary behaviors, is implicated in hastening weight gain, subsequently resulting in health complications such as obesity, diabetes, and cancer. To this end, it is vital to notice the deleterious consequences of the CAF regimen prior to the onset of complications, which is fundamental for early intervention in the context of numerous diseases. Probiotic-derived postbiotic metabolites have gained attention for their antioxidative properties, offering a potential countermeasure against oxidative stress. This research sought to discern the protective efficacy of SCD Probiotics against liver glutathione system damage arising from the CAF diet during developmental phases. Male Wistar rats, from weaning on day 21 to day 56, were categorized into four groups: a control on a conventional diet; a group on a standard diet enriched with SCD Probiotics; a mixed-diet group comprising both CAF and standard feed; and a combination diet group supplemented with SCD Probiotics. Through the application of real-time PCR, enzyme activity assessments, and quantitative metabolite analyses, our findings highlight the CAF diet's adverse influence on the liver's antioxidant defenses via shifts in gene expression. Yet, the inclusion of SCD Probiotics mostly ameliorated these harmful effects. Remarkably, the positive regulatory influence of SCD Probiotics on the liver's antioxidant system was consistently observed, independent of the CAF diet's presence.
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Affiliation(s)
- Nurdan Aba
- Department of Biology, Science Faculty, Muş Alparslan University, 49250 Mus, Turkey
| | - Enver Fehim Koçpınar
- Department of Medical Laboratory Techniques, Vocational School of Health Services, Muş Alparslan University, 49250 Mus, Turkey
| | - Taha Ceylani
- Department of Food Quality Control and Analysis, Muş Alparslan University, 49250 Mus, Turkey
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Chen CC, Yu TH, Wu CC, Hung WC, Lee TL, Tang WH, Tsai IT, Chung FM, Lee YJ, Hsu CC. Loss of ficolin-3 expression is associated with poor prognosis in patients with hepatocellular carcinoma. Int J Med Sci 2023; 20:1091-1096. [PMID: 37484802 PMCID: PMC10357436 DOI: 10.7150/ijms.84729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/21/2023] [Indexed: 07/25/2023] Open
Abstract
Background: Ficolin-3 (FCN3) is a well-known circulating pattern recognition molecule which plays a role in host immune responses to cancer via activation of the lectin complement pathway. Nevertheless, the clinical significance of FCN3 in patients with hepatocellular carcinoma (HCC) is unclear. Methods: Eighty-seven HCC patients who received hepatectomy at our hospital were included. Immunohistochemical staining was used to assess the FCN3 expression in both tumorous and non-tumorous tissues from the patients, who were classified into high and low expression groups. Differences in clinicopathological characteristics between the two groups were then analyzed. Results: Survival was significantly associated with FCN3 immunohistochemical score (p for trend = 0.048). Kaplan-Meier analysis revealed a higher overall survival rate in the patients with a high FCN3 expression than in those with a low FCN3 expression (p=0.031). A high FCN3 expression in tumor tissue was independently associated with better overall survival (p=0.042). However, multivariate analysis showed that FCN3 expression was not an independent risk factor for overall survival. Conclusion: Our findings suggest that FCN3 is significantly related to the prognosis of HCC. FCN3 may be a prognostic marker in patients with HCC.
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Affiliation(s)
- Chia-Chi Chen
- Department of Pathology, E-Da Hospital, I-Shou University, Kaohsiung 82445 Taiwan
- The School of Chinese Medicine for Post Baccalaureate, College of Medicine, I-Shou University, Kaohsiung 82445 Taiwan
- Department of Physical Therapy, I-Shou University, Kaohsiung 82445 Taiwan
- Department of Occupational therapy, I-Shou University, Kaohsiung 82445 Taiwan
| | - Teng-Hung Yu
- Division of Cardiology, Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung 82445 Taiwan
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 82445 Taiwan
| | - Cheng-Ching Wu
- Division of Cardiology, Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung 82445 Taiwan
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 82445 Taiwan
- Division of Cardiology, Department of Internal Medicine, E-Da Cancer Hospital, I-Shou University, Kaohsiung 82445 Taiwan
| | - Wei-Chin Hung
- Division of Cardiology, Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung 82445 Taiwan
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 82445 Taiwan
| | - Thung-Lip Lee
- Division of Cardiology, Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung 82445 Taiwan
- School of Medicine for International Students, College of Medicine, I-Shou University, Kaohsiung 82445 Taiwan
| | - Wei-Hua Tang
- Division of Cardiology, Department of Internal Medicine, Taipei Veterans General Hospital, Yuli Branch, Hualien 98142 Taiwan
- Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304 Taiwan
| | - I-Ting Tsai
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 82445 Taiwan
- Department of Emergency, E-Da Hospital, I-Shou University, Kaohsiung, 82445 Taiwan
| | - Fu-Mei Chung
- Division of Cardiology, Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung 82445 Taiwan
| | | | - Chia-Chang Hsu
- The School of Chinese Medicine for Post Baccalaureate, College of Medicine, I-Shou University, Kaohsiung 82445 Taiwan
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung 82445 Taiwan
- Health Examination Center, E-Da Dachang Hospital, I-Shou University, Kaohsiung 80794 Taiwan
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Wang LT, Zeng QL, Jiang SL, Chen ZY, Wang XL, Li L, Li X. Ficolin-2: A potential immune-related therapeutic target with low expression in liver cancer. Front Oncol 2022; 12:987481. [PMID: 36425563 PMCID: PMC9679423 DOI: 10.3389/fonc.2022.987481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/04/2022] [Indexed: 11/09/2022] Open
Abstract
Objective This study aimed to investigate the role of ficolin-2 (FCN2) in the development and course of hepatocellular carcinoma (HCC) and to contribute to the evolution of innovative HCC therapeutics. Methods Oncomine, GEPIA (Gene Expression Profiling Interactive Analysis), TISIDB (Tumor Immune System Interactions and Drug Bank database), UALCAN (University of Alabama at Birmingham Cancer data analysis portal), UCSC (University of California, Santa Cruz), R package, the Kaplan–Meier technique, Cox regression analysis, LinkedOmics, Pearson’s correlation, and a nomogram were used to investigate the prognostic value of FCN2 in HCC. Co-expressed genes were screened. A protein–protein interaction network was created using the STRING database. Finally, immunohistochemistry was performed to establish the expression of FCN2 in HCC tissues. A pan-cancer study centered on HCC-related molecular analysis was also conducted to look for a link between FCN2 and immune infiltration, immune modulators, and chemokine receptors. Results In HCC tissues, the expression of FCN2 was observed to be lower than that in normal tissues. This was connected to the HCC marker alpha-fetoprotein, showing that FCN2 is involved in the development and progression of cancer. FCN2 may act through Staphylococcus aureus infection, lectins, and other pathways. Furthermore, at the immune level, the expression of FCN2 in HCC was associated with some immune cell infiltration, immunomodulators, and chemokine receptors. Conclusion FCN2 may be an immune checkpoint inhibitor for HCC, creating a breakthrough in the treatment of HCC.
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Affiliation(s)
- Li-ting Wang
- The First Clinical College of Guangxi Medical University, Nanning, China
| | - Qiu-ling Zeng
- The First Clinical College of Guangxi Medical University, Nanning, China
| | - Shao-lan Jiang
- The First Clinical College of Guangxi Medical University, Nanning, China
| | - Zhen-yu Chen
- The First Clinical College of Guangxi Medical University, Nanning, China
| | - Xiao-ling Wang
- The First Clinical College of Guangxi Medical University, Nanning, China
| | - Ling Li
- Department of Pathology, The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- *Correspondence: Ling Li, ; Xiaolong Li,
| | - Xiaolong Li
- Department of Cell Biology and Genetics, Key Laboratory of Longevity and Agingrelated Diseases of Chinese Ministry of Education, School of Pre-Clinical Medicine, Guangxi Medical University, Nanning, China
- *Correspondence: Ling Li, ; Xiaolong Li,
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Elbakkoush AA, Khaleel A, Mohamed ANA, Alathamneh A. Pathway analysis of sepsis-induced changes gene expression. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00352-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Sepsis reaction is a response to an infection composed of genetic elements. This research aims to better understand how sepsis affects the molecular pathways in whole blood samples.
Methods
Whole blood samples from healthy controls (n = 18), sepsis nonsurvivors (n = 9), and sepsis survivors (n = 26) were retrieved from the gene expression omnibus (GEO) collection of the national center for biotechnology information (NCBI) (accession number GSE54514). The NCBI's GEO2R program was used to determine differential expression, and the ingenuity pathway analysis (IPA) software was utilized to do a pathway analysis.
Results
In sepsis patients, 2672 genes were substantially differently expressed (p value 0.05). One thousand three hundred four genes were overexpressed, and one thousand three hundred sixty-eight were under-expressed. The inhibition of ARE-mediated mRNA degradation pathway and the Pl3K/AKT signaling spliceosomal cycle were the most significant canonical pathways identified by ingenuity pathway analysis (IPA). The IPA upstream analysis predicted the ESR1, SIRT1, and PTPRR proteins, and the drugs filgrastim and fluticasone were top transcriptional regulators.
Conclusions
The inhibition of ARE-mediated mRNA degradation pathway and the Pl3K/AKT signaling spliceosomal cycle were highlighted as essential pathways of inflammation by IPA, indicating widespread cancer owing to sepsis. Our data imply that sepsis considerably influences gene pathways in whole blood samples, pointing to possible targets for sepsis treatment.
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Ávila C, Llebrés MT, Castro-Rodríguez V, Lobato-Fernández C, Reymond I, Harvengt L, Trontin JF, Cánovas FM. Identification of Metabolic Pathways Differentially Regulated in Somatic and Zygotic Embryos of Maritime Pine. FRONTIERS IN PLANT SCIENCE 2022; 13:877960. [PMID: 35665168 PMCID: PMC9159154 DOI: 10.3389/fpls.2022.877960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
Embryogenesis is a complex phase of conifer development involving hundreds of genes, and a proper understanding of this process is critical not only to produce embryos with different applied purposes but also for comparative studies with angiosperms. A global view of transcriptome dynamics during pine somatic and zygotic embryogenesis is currently missing. Here, we present a genome-wide transcriptome analysis of somatic and zygotic embryos at three developmental stages to identify conserved biological processes and gene functions during late embryogenesis. Most of the differences became more significant as the developmental process progressed from early to cotyledonary stages, and a higher number of genes were differentially expressed in somatic than in zygotic embryos. Metabolic pathways substantially affected included those involved in amino acid biosynthesis and utilization, and this difference was already observable at early developmental stages. Overall, this effect was found to be independent of the line (genotype) used to produce the somatic embryos. Additionally, transcription factors differentially expressed in somatic versus zygotic embryos were analyzed. Some potential hub regulatory genes were identified that can provide clues as to what transcription factors are controlling the process and to how the observed differences between somatic and zygotic embryogenesis in conifers could be regulated.
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Affiliation(s)
- Concepción Ávila
- Grupo de Biología Molecular y Biotecnología (BIO-114), Universidad de Málaga, Málaga, Spain
| | - María Teresa Llebrés
- Grupo de Biología Molecular y Biotecnología (BIO-114), Universidad de Málaga, Málaga, Spain
| | | | - César Lobato-Fernández
- Grupo de Biología Molecular y Biotecnología (BIO-114), Universidad de Málaga, Málaga, Spain
| | - Isabelle Reymond
- BioForBois, Pôle Industrie Bois Construction, Institut Technologique FCBA, Cestas, France
| | - Luc Harvengt
- BioForBois Laboratory, Pôle Industrie Bois Construction, Institut Technologique FCBA, Bordeaux, France
| | - Jean-François Trontin
- BioForBois, Pôle Industrie Bois Construction, Institut Technologique FCBA, Cestas, France
| | - Francisco M Cánovas
- Grupo de Biología Molecular y Biotecnología (BIO-114), Universidad de Málaga, Málaga, Spain
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A Novel Gene Signature Based on CDC20 and FCN3 for Prediction of Prognosis and Immune Features in Patients with Hepatocellular Carcinoma. J Immunol Res 2022; 2022:9117205. [PMID: 35402624 PMCID: PMC8986430 DOI: 10.1155/2022/9117205] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/02/2022] [Accepted: 03/05/2022] [Indexed: 11/18/2022] Open
Abstract
Long-term survivals of patients with hepatocellular carcinoma (HCC) remain unfavorable, which is largely attributed to active carcinogenesis. Growing studies have suggested that the reliable gene signature could act as an independent prognosis factor for HCC patients. We tried to screen the survival-related genes and develop a prognostic prediction model for HCC patients based on the expression profiles of the critical survival-related genes. In this study, we analyzed TCGA datasets and identified 280 genes with differential expressions (125 increased genes and 155 reduced genes). We analyzed the prognosis value of the top 10 dysregulated genes in HCC patients and identified three critical genes, including FCN3, CDC20, and E2F1, which were confirmed to be associated with long-term survival in both TCGA and ICGC datasets. The results of the LASSO model screened CDC20 and FCN3 for the development of the prognostic model. The CDC20 expression was distinctly increased in HCC specimens, while the FCN3 expression was distinctly decreased in HCC. At a suitable cutoff, patients were divided into low-risk and high-risk groups. Survival assays revealed that patients in high-risk groups exhibited a shorter overall survival than those in low-risk groups. Finally, we examine the relationships between risk score and immune infiltration abundance in HCC and observed that risk score was positively correlated with infiltration degree of B cells, T cell CD4+ cells, neutrophil, macrophage, and myeloid dendritic cells. Overall, we identified three critical survival-related genes and used CDC20 and FCN3 to develop a novel model for predicting outcomes and immune landscapes for patients with HCC. The above three genes also have a high potential for targeted cancer therapy of patients with HCC.
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Liu L, Liu Z, Meng L, Li L, Gao J, Yu S, Hu B, Yang H, Guo W, Zhang S. An Integrated Fibrosis Signature for Predicting Survival and Immunotherapy Efficacy of Patients With Hepatocellular Carcinoma. Front Mol Biosci 2022; 8:766609. [PMID: 34970594 PMCID: PMC8712696 DOI: 10.3389/fmolb.2021.766609] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/16/2021] [Indexed: 12/11/2022] Open
Abstract
Introduction: Fibrosis, a primary cause of hepatocellular carcinoma (HCC), is intimately associated with inflammation, the tumor microenvironment (TME), and multiple carcinogenic pathways. Currently, due to widespread inter- and intra-tumoral heterogeneity of HCC, the efficacy of immunotherapy is limited. Seeking a stable and novel tool to predict prognosis and immunotherapy response is imperative. Methods: Using stepwise Cox regression, least absolute shrinkage and selection operator (LASSO), and random survival forest algorithms, the fibrosis-associated signature (FAIS) was developed and further validated. Subsequently, comprehensive exploration was conducted to identify distinct genomic alterations, clinical features, biological functions, and immune landscapes of HCC patients. Results: The FAIS was an independent prognostic predictor of overall survival and recurrence-free survival in HCC. In parallel, the FAIS exhibited stable and accurate performance at predicting prognosis based on the evaluation of Kaplan-Meier survival curves, receiver operator characteristic curves, decision curve analysis, and Harrell's C-index. Further investigation elucidated that the high-risk group presented an inferior prognosis with advanced clinical traits and a high mutation frequency of TP53, whereas the low-risk group was characterized by superior CD8+ T cell infiltration, a higher TIS score, and a lower TIDE score. Additionally, patients in the low-risk group might yield more benefits from immunotherapy. Conclusion: The FAIS was an excellent scoring system that could stratify HCC patients and might serve as a promising tool to guide surveillance, improve prognosis, and facilitate clinical management.
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Affiliation(s)
- Long Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Research Centre for Organ Transplantation, Zhengzhou, China.,Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lingfang Meng
- Department of Infection Management, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lifeng Li
- Internet Medical and System Applications of National Engineering Laboratory, Zhengzhou, China
| | - Jie Gao
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Research Centre for Organ Transplantation, Zhengzhou, China.,Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Shizhe Yu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Research Centre for Organ Transplantation, Zhengzhou, China.,Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Bowen Hu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Research Centre for Organ Transplantation, Zhengzhou, China.,Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Han Yang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Research Centre for Organ Transplantation, Zhengzhou, China.,Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Research Centre for Organ Transplantation, Zhengzhou, China.,Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
| | - Shuijun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Research Centre for Organ Transplantation, Zhengzhou, China.,Henan Key Laboratory of Digestive Organ Transplantation, Zhengzhou, China
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Single-Cell Transcriptomics Reveals the Expression of Aging- and Senescence-Associated Genes in Distinct Cancer Cell Populations. Cells 2021; 10:cells10113126. [PMID: 34831349 PMCID: PMC8623328 DOI: 10.3390/cells10113126] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/31/2021] [Accepted: 11/09/2021] [Indexed: 12/12/2022] Open
Abstract
The human aging process is associated with molecular changes and cellular degeneration, resulting in a significant increase in cancer incidence with age. Despite their potential correlation, the relationship between cancer- and ageing-related transcriptional changes is largely unknown. In this study, we aimed to analyze aging-associated transcriptional patterns in publicly available bulk mRNA-seq and single-cell RNA-seq (scRNA-seq) datasets for chronic myelogenous leukemia (CML), colorectal cancer (CRC), hepatocellular carcinoma (HCC), lung cancer (LC), and pancreatic ductal adenocarcinoma (PDAC). Indeed, we detected that various aging/senescence-induced genes (ASIGs) were upregulated in malignant diseases compared to healthy control samples. To elucidate the importance of ASIGs during cell development, pseudotime analyses were performed, which revealed a late enrichment of distinct cancer-specific ASIG signatures. Notably, we were able to demonstrate that all cancer entities analyzed in this study comprised cell populations expressing ASIGs. While only minor correlations were detected between ASIGs and transcriptome-wide changes in PDAC, a high proportion of ASIGs was induced in CML, CRC, HCC, and LC samples. These unique cellular subpopulations could serve as a basis for future studies on the role of aging and senescence in human malignancies.
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