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Hernández-Lemus E, Ochoa S. Methods for multi-omic data integration in cancer research. Front Genet 2024; 15:1425456. [PMID: 39364009 PMCID: PMC11446849 DOI: 10.3389/fgene.2024.1425456] [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: 04/29/2024] [Accepted: 08/28/2024] [Indexed: 10/05/2024] Open
Abstract
Multi-omics data integration is a term that refers to the process of combining and analyzing data from different omic experimental sources, such as genomics, transcriptomics, methylation assays, and microRNA sequencing, among others. Such data integration approaches have the potential to provide a more comprehensive functional understanding of biological systems and has numerous applications in areas such as disease diagnosis, prognosis and therapy. However, quantitative integration of multi-omic data is a complex task that requires the use of highly specialized methods and approaches. Here, we discuss a number of data integration methods that have been developed with multi-omics data in view, including statistical methods, machine learning approaches, and network-based approaches. We also discuss the challenges and limitations of such methods and provide examples of their applications in the literature. Overall, this review aims to provide an overview of the current state of the field and highlight potential directions for future research.
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Affiliation(s)
- Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Center for Complexity Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Soledad Ochoa
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, United States
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Jeong EA, Lee MH, Bae AN, Kim J, Park JH, Lee JH. A Comprehensive Analysis of HOXB13 Expression in Hepatocellular Carcinoma. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:716. [PMID: 38792899 PMCID: PMC11123440 DOI: 10.3390/medicina60050716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024]
Abstract
Background and objectives: Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide and is caused by multiple factors. To explore novel targets for HCC treatment, we comprehensively analyzed the expression of HomeoboxB13 (HOXB13) and its role in HCC. Materials and Methods: The clinical significance of HCC was investigated using open gene expression databases, such as TIMER, UALCAN, KM, OSlihc, and LinkedOmics, and immunohistochemistry analysis. We also analyzed cell invasion and migration in HCC cell lines transfected with HOXB13-siRNA and their association with MMP9, E2F1, and MEIS1. Results: HOXB13 expression was higher in fibrolamellar carcinoma than in other histological subtypes. Its expression was associated with lymph node metastasis, histological stage, and tumor grade. It was positively correlated with immune cell infiltration of B cells (R = 0.246), macrophages (R = 0.182), myeloid dendritic cells (R = 0.247), neutrophils (R = 0.117), and CD4+ T cells (R = 0.258) and negatively correlated with immune cell infiltration of CD8+ T cells (R = -0.107). A positive correlation was observed between HOXB13, MMP9 (R = 0.176), E2F1 (R = 0.241), and MEIS1 (R = 0.189) expression (p < 0.001). The expression level of HOXB13 was significantly downregulated in both HepG2 and PLC/PFR/5 cell lines transfected with HOXB13-siRNA compared to that in cells transfected with NC siRNA (p < 0.05). Additionally, HOXB13 significantly affected cell viability and wound healing. Conclusions: HOXB13 overexpression may lead to poor prognosis in patients with HCC. Additional in vivo studies are required to improve our understanding of the biological role and the exact mechanism of action of HOXB13 in HCC.
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Affiliation(s)
- Eun-A Jeong
- Department of Anatomy, Keimyung University School of Medicine, Daegu 42601, Republic of Korea; (E.-A.J.); (A.-N.B.); (J.-H.P.)
| | - Moo-Hyun Lee
- Department of Surgery, Keimyung University School of Medicine, Daegu 42601, Republic of Korea;
| | - An-Na Bae
- Department of Anatomy, Keimyung University School of Medicine, Daegu 42601, Republic of Korea; (E.-A.J.); (A.-N.B.); (J.-H.P.)
| | - Jongwan Kim
- Department of Biomedical Laboratory Science, Dong-Eui Institute of Technology, 54 Yangji-ro, Busan 47230, Republic of Korea;
| | - Jong-Ho Park
- Department of Anatomy, Keimyung University School of Medicine, Daegu 42601, Republic of Korea; (E.-A.J.); (A.-N.B.); (J.-H.P.)
| | - Jae-Ho Lee
- Department of Anatomy, Keimyung University School of Medicine, Daegu 42601, Republic of Korea; (E.-A.J.); (A.-N.B.); (J.-H.P.)
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Gholizadeh M, Mazlooman SR, Hadizadeh M, Drozdzik M, Eslami S. Detection of key mRNAs in liver tissue of hepatocellular carcinoma patients based on machine learning and bioinformatics analysis. MethodsX 2023; 10:102021. [PMID: 36713306 PMCID: PMC9879787 DOI: 10.1016/j.mex.2023.102021] [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: 08/17/2022] [Accepted: 01/15/2023] [Indexed: 01/19/2023] Open
Abstract
One methodology extensively used to develop biomarkers is the precise detection of highly responsive genes that can distinguish cancer samples from healthy samples. The purpose of this study was to screen for potential hepatocellular carcinoma (HCC) biomarkers based on non-fusion integrative multi-platform meta-analysis method. The gene expression profiles of liver tissue samples from two microarray platforms were initially analyzed using a meta-analysis based on an empirical Bayesian method to robust discover differentially expressed genes in HCC and non-tumor tissues. Then, using the bioinformatics technique of weighted correlation network analysis, the highly associated prioritized Differentially Expressed Genes (DEGs) were clustered. Co-expression network and topological analysis were utilized to identify sub-clusters and confirm candidate genes. Next, a diagnostic model was developed and validated using a machine learning algorithm. To construct a prognostic model, the Cox proportional hazard regression analysis was applied and validated. We identified three genes as specific biomarkers for the diagnosis of HCC based on accuracy and feasibility. The diagnostic model's area under the curve was 0.931 with confidence interval of 0.923-0.952.•Non-fusion integrative multi-platform meta-analysis method.•Classification methods and biomarkers recognition via machine learning method.•Biomarker validation models.
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Affiliation(s)
- Maryam Gholizadeh
- Department of Medical Informatics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 91388-13944, Iran
| | - Seyed Reza Mazlooman
- Department of Computer Engineering, Central Tehran Branch, Islamic Azad University, Tehran 1477893780, Iran
| | - Morteza Hadizadeh
- Physiology Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman 7616913555, Iran
| | - Marek Drozdzik
- Department of Experimental and Clinical Pharmacology, Pomeranian Medical University, Szczecin 70-111, Poland
| | - Saeid Eslami
- Department of Medical Informatics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 91388-13944, Iran
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Usman M, Hameed Y, Ahmad M, Iqbal MJ, Maryam A, Mazhar A, Naz S, Tanveer R, Saeed H, Bint-E-Fatima, Ashraf A, Hadi A, Hameed Z, Tariq E, Aslam AS. SHMT2 is Associated with Tumor Purity, CD8+ T Immune Cells Infiltration, and a Novel Therapeutic Target in Four Different Human Cancers. Curr Mol Med 2023; 23:161-176. [PMID: 35023455 DOI: 10.2174/1566524022666220112142409] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 11/15/2021] [Accepted: 11/25/2021] [Indexed: 12/16/2022]
Abstract
AIMS This study was launched to identify the SHMT2 associated Human Cancer subtypes. BACKGROUND Cancer is the 2nd leading cause of death worldwide. Previous reports revealed the limited involvement of SHMT2 in human cancer. In the current study, we comprehensively analyzed the role of SHMT2 in 24 major subtypes of human cancers using in silico approach and identified a few subtypes that are mainly associated with SHMT2. OBJECTIVE We aim to comprehensively analyze the role of SHMT2 in 24 major subtypes of human cancers using in silico approach and identified a few subtypes that are mainly associated with SHMT2. Earlier, limited knowledge exists in the medical literature regarding the involvement of Serine Hydroxymethyltransferase 2 (SHMT2) in human cancer. METHODS In the current study, we comprehensively analyzed the role of SHMT2 in 24 major subtypes of human cancers using in silico approach and identified a few subtypes that are mainly associated with SHMT2. Pan-cancer transcriptional expression profiling of SHMT2 was done using UALCAN while further validation was performed using GENT2. For translational profiling of SHMT2, we utilized Human Protein Atlas (HPA) platform. Promoter methylation, genetic alteration, and copy number variations (CNVs) profiles were analyzed through MEXPRESS and cBioPortal. Survival analysis was carried out through Kaplan-Meier (KM) plotter platform. Pathway enrichment analysis of SHMT2 was performed using DAVID, while the gene-drug network was drawn through CTD and Cytoscape. Furthermore, in the tumor microenvironment, a correlation between tumor purity, CD8+ T immune cells infiltration, and SHMT2 expression was accessed using TIMER. RESULTS SHMT2 was found overexpressed in 24 different subtypes of human cancers and its overexpression was significantly associated with the reduced Overall survival (OS) and Relapse-free survival durations of Breast cancer (BRCA), Kidney renal papillary cell carcinoma (KIRP), Liver hepatocellular carcinoma (LIHC), and Lung adenocarcinoma (LUAD) patients. This implies that SHMT2 plays a significant role in the development and progression of these cancers. We further noticed that SHMT2 was also up-regulated in BRCA, KIRP, LIHC, and LUAD patients of different clinicopathological features. Pathways enrichment analysis revealed the involvement of SHMT2 enriched genes in five diverse pathways. Furthermore, we also explored some interesting correlations between SHMT2 expression and promoter methylation, genetic alterations, CNVs, tumor purity, and CD8+ T immune cell infiltrates. CONCLUSION Our results suggested that overexpressed SHMT2 is correlated with the reduced OS and RFS of the BRCA, KIRP, LIHC, and LUAD patients and can be a potential diagnostic and prognostic biomarker for these cancers.
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Affiliation(s)
- Muhammad Usman
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Yasir Hameed
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Mukhtiar Ahmad
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | | | - Aghna Maryam
- Department of Biochemistry, Quaid-i-Azam University Islamabad, Pakistan
| | - Afshan Mazhar
- Department of Biochemistry, Quaid-i-Azam University Islamabad, Pakistan
| | - Saima Naz
- Department of zoology, Government Sadiq College Women University Bahawalpur, Bahawalpur, Pakistan
| | - Rida Tanveer
- University College of Conventional Medicine, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Hina Saeed
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Bint-E-Fatima
- Department of Biotechnology, University of Gujrat, Gujrat, Pakistan
| | - Aneela Ashraf
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Alishba Hadi
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Zahid Hameed
- Department of Bioinformatics and Biotechnology, International Islamic University Islamabad, Islamabad, Pakistan
| | - Eman Tariq
- Department of Chemistry, The University of Swabi, Swabi, Pakistan
| | - Alia Sumyya Aslam
- Department of Biochemistry and Biotechnology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
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Zhu HX, Lu WJ, Zhu WP, Yu S. Comprehensive analysis of N 6 -methyladenosine-related long non-coding RNAs for prognosis prediction in liver hepatocellular carcinoma. J Clin Lab Anal 2021; 35:e24071. [PMID: 34741346 PMCID: PMC8649367 DOI: 10.1002/jcla.24071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/28/2021] [Accepted: 10/08/2021] [Indexed: 12/24/2022] Open
Abstract
Background Liver hepatocellular carcinoma (LIHC) is a lethal cancer. This study aimed to identify the N6‐methyladenosine (m6A)‐targeted long non‐coding RNA (lncRNA) related to LIHC prognosis and to develop an m6A‐targeted lncRNA model for prognosis prediction in LIHC. Methods The expression matrix of mRNA and lncRNA was obtained, and differentially expressed (DE) mRNAs and lncRNAs between tumor and normal samples were identified. Univariate Cox and pathway enrichment analyses were performed on the m6A‐targeted lncRNAs and the LIHC prognosis‐related m6A‐targeted lncRNAs. Prognostic analysis, immune infiltration, and gene DE analyses were performed on LIHC subgroups, which were obtained from unsupervised clustering analysis. Additionally, a multi‐factor Cox analysis was used to construct a prognostic risk model based on the lncRNAs from the LASSO Cox model. Univariate and multivariate Cox analyses were used to assess prognostic independence. Results A total of 5031 significant DEmRNAs and 292 significant DElncRNAs were screened, and 72 LIHC‐specific m6A‐targeted binding lncRNAs were screened. Moreover, a total of 29 LIHC prognosis‐related m6A‐targeted lncRNAs were obtained and enriched in cytoskeletal, spliceosome, and cell cycle pathways. An 11‐m6A‐lncRNA prognostic model was constructed and verified; the top 10 lncRNAs included LINC00152, RP6‐65G23.3, RP11‐620J15.3, RP11‐290F5.1, RP11‐147L13.13, RP11‐923I11.6, AC092171.4, KB‐1460A1.5, LINC00339, and RP11‐119D9.1. Additionally, the two LIHC subgroups, Cluster 1 and Cluster 2, showed significant differences in the immune microenvironment, m6A enzyme genes, and prognosis of LIHC. Conclusion The m6A‐lncRNA prognostic model accurately and effectively predicted the prognostic survival of LIHC. Immune cells, immune checkpoints (ICs), and m6A enzyme genes could act as novel therapeutic targets for LIHC.
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Affiliation(s)
- Hong-Xu Zhu
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wen-Jie Lu
- Department of General Surgery, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Wei-Ping Zhu
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
| | - Song Yu
- Department of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
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Fusco N, Marchiò C, Ghidini M, Scatena C. Special Issue: Molecular Biomarkers in Solid Tumors. Genes (Basel) 2021; 12:genes12070984. [PMID: 34203156 PMCID: PMC8304302 DOI: 10.3390/genes12070984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 06/24/2021] [Indexed: 11/16/2022] Open
Affiliation(s)
- Nicola Fusco
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
- Correspondence: (N.F.); (C.M.); (M.G.); (C.S.)
| | - Caterina Marchiò
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy
- Division of Pathology, Candiolo Cancer Institute FPO-IRCCS, 10060 Candiolo, Italy
- Correspondence: (N.F.); (C.M.); (M.G.); (C.S.)
| | - Michele Ghidini
- Division of Medical Oncology, Fondazione IRCCS Ca’ Granda—Ospedale Maggiore Policlinico, 20122 Milan, Italy
- Correspondence: (N.F.); (C.M.); (M.G.); (C.S.)
| | - Cristian Scatena
- Division of Pathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy
- Correspondence: (N.F.); (C.M.); (M.G.); (C.S.)
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