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Hashemi Gheinani A, Kim J, You S, Adam RM. Bioinformatics in urology - molecular characterization of pathophysiology and response to treatment. Nat Rev Urol 2024; 21:214-242. [PMID: 37604982 DOI: 10.1038/s41585-023-00805-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2023] [Indexed: 08/23/2023]
Abstract
The application of bioinformatics has revolutionized the practice of medicine in the past 20 years. From early studies that uncovered subtypes of cancer to broad efforts spearheaded by the Cancer Genome Atlas initiative, the use of bioinformatics strategies to analyse high-dimensional data has provided unprecedented insights into the molecular basis of disease. In addition to the identification of disease subtypes - which enables risk stratification - informatics analysis has facilitated the identification of novel risk factors and drivers of disease, biomarkers of progression and treatment response, as well as possibilities for drug repurposing or repositioning; moreover, bioinformatics has guided research towards precision and personalized medicine. Implementation of specific computational approaches such as artificial intelligence, machine learning and molecular subtyping has yet to become widespread in urology clinical practice for reasons of cost, disruption of clinical workflow and need for prospective validation of informatics approaches in independent patient cohorts. Solving these challenges might accelerate routine integration of bioinformatics into clinical settings.
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Affiliation(s)
- Ali Hashemi Gheinani
- Department of Urology, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Urology, Inselspital, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Jina Kim
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sungyong You
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Rosalyn M Adam
- Department of Urology, Boston Children's Hospital, Boston, MA, USA.
- Department of Surgery, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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2
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Jeong E, Yoon S. Current advances in comprehensive omics data mining for oncology and cancer research. Biochim Biophys Acta Rev Cancer 2024; 1879:189030. [PMID: 38008264 DOI: 10.1016/j.bbcan.2023.189030] [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: 02/08/2023] [Revised: 09/05/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
The availability of a large amount of multiomics data enables data-driven discovery studies on cancers. High-throughput data on mutations, gene/protein expression, immune scores (tumor-infiltrating cells), drug screening, and RNAi (shRNAs and CRISPRs) screening are major integrated components of patient samples and cell line datasets. Improvements in data access and user interfaces make it easy for general scientists to carry out their data mining practices on integrated multiomics data platforms without computational expertise. Here, we summarize the extent of data integration and functionality of several portals and software that provide integrated multiomics data mining platforms for all cancer studies. Recent progress includes programming interfaces (APIs) for customized data mining. Precalculated datasets assist noncomputational users in quickly browsing data associations. Furthermore, stand-alone software provides fast calculations and smart functions, guiding optimal sampling and filtering options for the easy discovery of significant data associations. These efforts improve the utility of cancer omics big data for noncomputational users at all levels of cancer research. In the present review, we aim to provide analytical information guiding general scientists to find and utilize data mining tools for their research.
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Affiliation(s)
- Euna Jeong
- Research Institute of Women's Health, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Sukjoon Yoon
- Research Institute of Women's Health, Sookmyung Women's University, Seoul 04310, Republic of Korea; Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea.
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3
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Liu Y, Yin Z, Wang Y, Chen H. Exploration and validation of key genes associated with early lymph node metastasis in thyroid carcinoma using weighted gene co-expression network analysis and machine learning. Front Endocrinol (Lausanne) 2023; 14:1247709. [PMID: 38144565 PMCID: PMC10739373 DOI: 10.3389/fendo.2023.1247709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/17/2023] [Indexed: 12/26/2023] Open
Abstract
Background Thyroid carcinoma (THCA), the most common endocrine neoplasm, typically exhibits an indolent behavior. However, in some instances, lymph node metastasis (LNM) may occur in the early stages, with the underlying mechanisms not yet fully understood. Materials and methods LNM potential was defined as the tumor's capability to metastasize to lymph nodes at an early stage, even when the tumor volume is small. We performed differential expression analysis using the 'Limma' R package and conducted enrichment analyses using the Metascape tool. Co-expression networks were established using the 'WGCNA' R package, with the soft threshold power determined by the 'pickSoftThreshold' algorithm. For unsupervised clustering, we utilized the 'ConsensusCluster Plus' R package. To determine the topological features and degree centralities of each node (protein) within the Protein-Protein Interaction (PPI) network, we used the CytoNCA plugin integrated with the Cytoscape tool. Immune cell infiltration was assessed using the Immune Cell Abundance Identifier (ImmuCellAI) database. We applied the Least Absolute Shrinkage and Selection Operator (LASSO), Support Vector Machine (SVM), and Random Forest (RF) algorithms individually, with the 'glmnet,' 'e1071,' and 'randomForest' R packages, respectively. Ridge regression was performed using the 'oncoPredict' algorithm, and all the predictions were based on data from the Genomics of Drug Sensitivity in Cancer (GDSC) database. To ascertain the protein expression levels and subcellular localization of genes, we consulted the Human Protein Atlas (HPA) database. Molecular docking was carried out using the mcule 1-click Docking server online. Experimental validation of gene and protein expression levels was conducted through Real-Time Quantitative PCR (RT-qPCR) and immunohistochemistry (IHC) assays. Results Through WGCNA and PPI network analysis, we identified twelve hub genes as the most relevant to LNM potential from these two modules. These 12 hub genes displayed differential expression in THCA and exhibited significant correlations with the downregulation of neutrophil infiltration, as well as the upregulation of dendritic cell and macrophage infiltration, along with activation of the EMT pathway in THCA. We propose a novel molecular classification approach and provide an online web-based nomogram for evaluating the LNM potential of THCA (http://www.empowerstats.net/pmodel/?m=17617_LNM). Machine learning algorithms have identified ERBB3 as the most critical gene associated with LNM potential in THCA. ERBB3 exhibits high expression in patients with THCA who have experienced LNM or have advanced-stage disease. The differential methylation levels partially explain this differential expression of ERBB3. ROC analysis has identified ERBB3 as a diagnostic marker for THCA (AUC=0.89), THCA with high LNM potential (AUC=0.75), and lymph nodes with tumor metastasis (AUC=0.86). We have presented a comprehensive review of endocrine disruptor chemical (EDC) exposures, environmental toxins, and pharmacological agents that may potentially impact LNM potential. Molecular docking revealed a docking score of -10.1 kcal/mol for Lapatinib and ERBB3, indicating a strong binding affinity. Conclusion In conclusion, our study, utilizing bioinformatics analysis techniques, identified gene modules and hub genes influencing LNM potential in THCA patients. ERBB3 was identified as a key gene with therapeutic implications. We have also developed a novel molecular classification approach and a user-friendly web-based nomogram tool for assessing LNM potential. These findings pave the way for investigations into the mechanisms underlying differences in LNM potential and provide guidance for personalized clinical treatment plans.
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Affiliation(s)
- Yanyan Liu
- Department of General Surgery, The Third Affiliated Hospital of Anhui Medical University (The First People’s Hospital of Hefei), Hefei, Anhui, China
| | - Zhenglang Yin
- Department of General Surgery, The Third Affiliated Hospital of Anhui Medical University (The First People’s Hospital of Hefei), Hefei, Anhui, China
| | - Yao Wang
- Digestive Endoscopy Department, Jiangsu Province Hospital, The First Affiliated Hospital with Nanjing Medical University, Nanjing, Jiangsu, China
| | - Haohao Chen
- Department of General Surgery, The Third Affiliated Hospital of Anhui Medical University (The First People’s Hospital of Hefei), Hefei, Anhui, China
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4
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Wang J, Wang H, Xu J, Song Q, Zhou B, Shangguan J, Xue M, Wang Y. Identification of protein signatures for lung cancer subtypes based on BPSO method. PLoS One 2023; 18:e0294243. [PMID: 38060494 PMCID: PMC10703216 DOI: 10.1371/journal.pone.0294243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/27/2023] [Indexed: 12/18/2023] Open
Abstract
The objective of this study was to identify protein biomarkers that can distinguish between LUAD and LUSC, critical for personalized treatment plans. The proteomic profiling data of LUAD and LUSC samples from TCPA database, along with phenotype and survival information from TCGA database were downloaded and preprocessed for analysis. We used BPSO feature selection method and identified 10 candidate protein biomarkers that have better classifying performance, as analyzed by t-SNE and PCA algorithms. To explore the causalities among these proteins and their associations with tumor subtypes, we conducted the PCStable algorithm to construct a regulatory network. Results indicated that 4 proteins, MIG6, CD26, NF2, and INPP4B, were directly linked to the lung cancer subtypes and may be useful in guiding therapeutic decision-making. Besides, spearman correlation, Cox proportional hazard model and Kaplan-Meier curve was employed to validate the biological significance of the candidate proteins. In summary, our study highlights the importance of protein biomarkers in the classification of lung cancer subtypes and the potential of computational methods for identifying key biomarkers and understanding their underlying biological mechanisms.
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Affiliation(s)
- Jihan Wang
- Department of Basic Medicine, School of Medicine, Xi’an International University, Xi’an, 710077, China
| | - Hanping Wang
- Department of Basic Medicine, School of Medicine, Xi’an International University, Xi’an, 710077, China
- Engineering Research Center of Personalized Anti-aging Health Product Development and Transformation, Universities of Shaanxi Province, Xi’an, 710077, China
| | - Jing Xu
- Department of Basic Medicine, School of Medicine, Xi’an International University, Xi’an, 710077, China
| | - Qiying Song
- Department of Basic Medicine, School of Medicine, Xi’an International University, Xi’an, 710077, China
| | - Baozhen Zhou
- Department of Basic Medicine, School of Medicine, Xi’an International University, Xi’an, 710077, China
| | - Jingbo Shangguan
- Department of Basic Medicine, School of Medicine, Xi’an International University, Xi’an, 710077, China
| | - Mengju Xue
- Department of Basic Medicine, School of Medicine, Xi’an International University, Xi’an, 710077, China
| | - Yangyang Wang
- School of Electronics and Information, Northwestern Polytechnical University, Xi’an, 710129, China
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5
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Chen C, Liu Y, Li Q, Zhang Z, Luo M, Liu Y, Han L. The Genetic, Pharmacogenomic, and Immune Landscapes Associated with Protein Expression across Human Cancers. Cancer Res 2023; 83:3673-3680. [PMID: 37548539 PMCID: PMC10843800 DOI: 10.1158/0008-5472.can-23-0758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/15/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
Proteomics is a powerful approach that can rapidly enhance our understanding of cancer development. Detailed characterization of the genetic, pharmacogenomic, and immune landscape in relation to protein expression in patients with cancer could provide new insights into the functional roles of proteins in cancer. By taking advantage of the genotype data from The Cancer Genome Atlas and protein expression data from The Cancer Proteome Atlas, we characterized the effects of genetic variants on protein expression across 31 cancer types and identified approximately 100,000 protein quantitative trait loci (pQTL). Among these, over 8000 pQTLs were associated with patient overall survival. Furthermore, characterization of the impact of protein expression on more than 350 imputed anticancer drug responses in patients revealed nearly 230,000 significant associations. In addition, approximately 21,000 significant associations were identified between protein expression and immune cell abundance. Finally, a user-friendly data portal, GPIP (https://hanlaboratory.com/GPIP), was developed featuring multiple modules that enable researchers to explore, visualize, and browse multidimensional data. This detailed analysis reveals the associations between the proteomic landscape and genetic variation, patient outcome, the immune microenvironment, and drug response across cancer types, providing a resource that may offer valuable clinical insights and encourage further functional investigations of proteins in cancer. SIGNIFICANCE Comprehensive characterization of the relationship between protein expression and the genetic, pharmacogenomic, and immune landscape of tumors across cancer types provides a foundation for investigating the role of protein expression in cancer development and treatment.
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Affiliation(s)
- Chengxuan Chen
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN, USA
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Yuan Liu
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN, USA
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Qiang Li
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Zhao Zhang
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Mei Luo
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN, USA
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Yaoming Liu
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Leng Han
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, IN, USA
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
- Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, USA
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6
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Lei JT, Jaehnig EJ, Smith H, Holt MV, Li X, Anurag M, Ellis MJ, Mills GB, Zhang B, Labrie M. The Breast Cancer Proteome and Precision Oncology. Cold Spring Harb Perspect Med 2023; 13:a041323. [PMID: 37137501 PMCID: PMC10547392 DOI: 10.1101/cshperspect.a041323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The goal of precision oncology is to translate the molecular features of cancer into predictive and prognostic tests that can be used to individualize treatment leading to improved outcomes and decreased toxicity. Success for this strategy in breast cancer is exemplified by efficacy of trastuzumab in tumors overexpressing ERBB2 and endocrine therapy for tumors that are estrogen receptor positive. However, other effective treatments, including chemotherapy, immune checkpoint inhibitors, and CDK4/6 inhibitors are not associated with strong predictive biomarkers. Proteomics promises another tier of information that, when added to genomic and transcriptomic features (proteogenomics), may create new opportunities to improve both treatment precision and therapeutic hypotheses. Here, we review both mass spectrometry-based and antibody-dependent proteomics as complementary approaches. We highlight how these methods have contributed toward a more complete understanding of breast cancer and describe the potential to guide diagnosis and treatment more accurately.
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Affiliation(s)
- Jonathan T Lei
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Eric J Jaehnig
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hannah Smith
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Matthew V Holt
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xi Li
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Meenakshi Anurag
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Gordon B Mills
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Marilyne Labrie
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon 97239, USA
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Vishnoi M, Dereli Z, Yin Z, Kong EK, Kinali M, Thapa K, Babur O, Yun K, Abdelfattah N, Li X, Bozorgui B, Rostomily RC, Korkut A. A prognostic matrix code defines functional glioblastoma phenotypes and niches. RESEARCH SQUARE 2023:rs.3.rs-3285842. [PMID: 37790408 PMCID: PMC10543369 DOI: 10.21203/rs.3.rs-3285842/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Interactions among tumor, immune and vascular niches play major roles in driving glioblastoma (GBM) malignancy and treatment responses. The composition, heterogeneity, and localization of extracellular core matrix proteins (CMPs) that mediate such interactions, however, are not well understood. Here, we characterize functional and clinical relevance of genes encoding CMPs in GBM at bulk, single cell, and spatial anatomical resolution. We identify a "matrix code" for genes encoding CMPs whose expression levels categorize GBM tumors into matrisome-high and matrisome-low groups that correlate with worse and better patient survival, respectively. The matrisome enrichment is associated with specific driver oncogenic alterations, mesenchymal state, infiltration of pro-tumor immune cells and immune checkpoint gene expression. Anatomical and single cell transcriptome analyses indicate that matrisome gene expression is enriched in vascular and leading edge/infiltrative anatomic structures that are known to harbor glioma stem cells driving GBM progression. Finally, we identified a 17-gene matrisome signature that retains and further refines the prognostic value of genes encoding CMPs and, importantly, potentially predicts responses to PD1 blockade in clinical trials for GBM. The matrisome gene expression profiles provide potential biomarkers of functionally relevant GBM niches that contribute to mesenchymal-immune cross talk and patient stratification which could be applied to optimize treatment responses.
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Affiliation(s)
- Monika Vishnoi
- Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, 77030 USA
- Department of Neurosurgery, University of Washington School of Medicine, Seattle WA, 98195
| | - Zeynep Dereli
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zheng Yin
- Department of Systems Medicine and Bioengineering, Houston Methodist Neal Cancer Center, Houston, TX, 77030 USA
| | - Elisabeth K. Kong
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Statistics, Rice University, Houston, TX, 77030, USA
| | - Meric Kinali
- Computer Science, College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, 02125
| | - Kisan Thapa
- Computer Science, College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, 02125
| | - Ozgun Babur
- Computer Science, College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, 02125
| | - Kyuson Yun
- Department of Neurology, Houston Methodist Research Institute, Houston, TX, 77030 USA
- Department of Neurology, Weill Cornell Medical School, New York NY, 10065
| | - Nourhan Abdelfattah
- Department of Neurology, Houston Methodist Research Institute, Houston, TX, 77030 USA
- Department of Neurology, Weill Cornell Medical School, New York NY, 10065
| | - Xubin Li
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Behnaz Bozorgui
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert C. Rostomily
- Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, 77030 USA
- Department of Neurosurgery, University of Washington School of Medicine, Seattle WA, 98195
- Department of Neurosurgery, Weill Cornell Medical School, New York NY, 10065
| | - Anil Korkut
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
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8
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Upadhya SR, Ryan CJ. Antibody reliability influences observed mRNA-protein correlations in tumour samples. Life Sci Alliance 2023; 6:e202201885. [PMID: 37169592 PMCID: PMC10176110 DOI: 10.26508/lsa.202201885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023] Open
Abstract
Reverse phase protein arrays (RPPA) have been used to quantify the abundance of hundreds of proteins across thousands of tumour samples in the Cancer Genome Atlas. By number of samples, this is the largest tumour proteomic dataset available and it provides an opportunity to systematically assess the correlation between mRNA and protein abundances. However, the RPPA approach is highly dependent on antibody reliability and approximately one-quarter of the antibodies used in the the Cancer Genome Atlas are deemed to be somewhat less reliable. Here, we assess the impact of antibody reliability on observed mRNA-protein correlations. We find that, in general, proteins measured with less reliable antibodies have lower observed mRNA-protein correlations. This is not true of the same proteins when measured using mass spectrometry. Furthermore, in cell lines, we find that when the same protein is quantified by both mass spectrometry and RPPA, the overall correlation between the two measurements is lower for proteins measured with less reliable antibodies. Overall our results reinforce the need for caution in using RPPA measurements from less reliable antibodies.
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Affiliation(s)
- Swathi Ramachandra Upadhya
- School of Computer Science, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | - Colm J Ryan
- School of Computer Science, University College Dublin, Dublin, Ireland
- Conway Institute, University College Dublin, Dublin, Ireland
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
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Vishnoi M, Dereli Z, Yin Z, Kong EK, Kinali M, Thapa K, Babur O, Yun K, Abdelfattah N, Li X, Bozorgui B, Rostomily RC, Korkut A. A prognostic matrix code defines functional glioblastoma phenotypes and niches. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543903. [PMID: 37333072 PMCID: PMC10274725 DOI: 10.1101/2023.06.06.543903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Interactions among tumor, immune and vascular niches play major roles in driving glioblastoma (GBM) malignancy and treatment responses. The composition, heterogeneity, and localization of extracellular core matrix proteins (CMPs) that mediate such interactions, however, are not well understood. Here, we characterize functional and clinical relevance of genes encoding CMPs in GBM at bulk, single cell, and spatial anatomical resolution. We identify a "matrix code" for genes encoding CMPs whose expression levels categorize GBM tumors into matrisome-high and matrisome-low groups that correlate with worse and better survival, respectively, of patients. The matrisome enrichment is associated with specific driver oncogenic alterations, mesenchymal state, infiltration of pro-tumor immune cells and immune checkpoint gene expression. Anatomical and single cell transcriptome analyses indicate that matrisome gene expression is enriched in vascular and leading edge/infiltrative anatomic structures that are known to harbor glioma stem cells driving GBM progression. Finally, we identified a 17-gene matrisome signature that retains and further refines the prognostic value of genes encoding CMPs and, importantly, potentially predicts responses to PD1 blockade in clinical trials for GBM. The matrisome gene expression profiles may provide biomarkers of functionally relevant GBM niches that contribute to mesenchymal-immune cross talk and patient stratification to optimize treatment responses.
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Affiliation(s)
- Monika Vishnoi
- Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, 77030 USA
- Department of Neurosurgery, University of Washington School of Medicine, Seattle WA, 98195
| | - Zeynep Dereli
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zheng Yin
- Department of Systems Medicine and Bioengineering, Houston Methodist Neal Cancer Center, Houston, TX, 77030 USA
| | - Elisabeth K. Kong
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Statistics, Rice University, Houston, TX, 77030, USA
| | - Meric Kinali
- Computer Science, College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, 02125
| | - Kisan Thapa
- Computer Science, College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, 02125
| | - Ozgun Babur
- Computer Science, College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, 02125
| | - Kyuson Yun
- Department of Neurology, Houston Methodist Research Institute, Houston, TX, 77030 USA
- Department of Neurology, Weill Cornell Medical School, New York NY, 10065
| | - Nourhan Abdelfattah
- Department of Neurology, Houston Methodist Research Institute, Houston, TX, 77030 USA
- Department of Neurology, Weill Cornell Medical School, New York NY, 10065
| | - Xubin Li
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Behnaz Bozorgui
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert C. Rostomily
- Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, 77030 USA
- Department of Neurosurgery, University of Washington School of Medicine, Seattle WA, 98195
- Department of Neurosurgery, Weill Cornell Medical School, New York NY, 10065
| | - Anil Korkut
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
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10
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Ahmed F, Samantasinghar A, Manzoor Soomro A, Kim S, Hyun Choi K. A systematic review of computational approaches to understand cancer biology for informed drug repurposing. J Biomed Inform 2023; 142:104373. [PMID: 37120047 DOI: 10.1016/j.jbi.2023.104373] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/25/2023] [Accepted: 04/23/2023] [Indexed: 05/01/2023]
Abstract
Cancer is the second leading cause of death globally, trailing only heart disease. In the United States alone, 1.9 million new cancer cases and 609,360 deaths were recorded for 2022. Unfortunately, the success rate for new cancer drug development remains less than 10%, making the disease particularly challenging. This low success rate is largely attributed to the complex and poorly understood nature of cancer etiology. Therefore, it is critical to find alternative approaches to understanding cancer biology and developing effective treatments. One such approach is drug repurposing, which offers a shorter drug development timeline and lower costs while increasing the likelihood of success. In this review, we provide a comprehensive analysis of computational approaches for understanding cancer biology, including systems biology, multi-omics, and pathway analysis. Additionally, we examine the use of these methods for drug repurposing in cancer, including the databases and tools that are used for cancer research. Finally, we present case studies of drug repurposing, discussing their limitations and offering recommendations for future research in this area.
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Affiliation(s)
- Faheem Ahmed
- Department of Mechatronics Engineering, Jeju National University, Republic of Korea
| | | | | | - Sejong Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea; Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.
| | - Kyung Hyun Choi
- Department of Mechatronics Engineering, Jeju National University, Republic of Korea.
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Wang Y, Gao X, Wang J. Functional Proteomic Profiling Analysis in Four Major Types of Gastrointestinal Cancers. Biomolecules 2023; 13:biom13040701. [PMID: 37189448 DOI: 10.3390/biom13040701] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/05/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Gastrointestinal (GI) cancer accounts for one in four cancer cases and one in three cancer-related deaths globally. A deeper understanding of cancer development mechanisms can be applied to cancer medicine. Comprehensive sequencing applications have revealed the genomic landscapes of the common types of human cancer, and proteomics technology has identified protein targets and signalling pathways related to cancer growth and progression. This study aimed to explore the functional proteomic profiles of four major types of GI tract cancer based on The Cancer Proteome Atlas (TCPA). We provided an overview of functional proteomic heterogeneity by performing several approaches, including principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), t-stochastic neighbour embedding (t-SNE) analysis, and hierarchical clustering analysis in oesophageal carcinoma (ESCA), stomach adenocarcinoma (STAD), colon adenocarcinoma (COAD), and rectum adenocarcinoma (READ) tumours, to gain a system-wide understanding of the four types of GI cancer. The feature selection approach, mutual information feature selection (MIFS) method, was conducted to screen candidate protein signature subsets to better distinguish different cancer types. The potential clinical implications of candidate proteins in terms of tumour progression and prognosis were also evaluated based on TCPA and The Cancer Genome Atlas (TCGA) databases. The results suggested that functional proteomic profiling can identify different patterns among the four types of GI cancers and provide candidate proteins for clinical diagnosis and prognosis evaluation. We also highlighted the application of feature selection approaches in high-dimensional biological data analysis. Overall, this study could improve the understanding of the complexity of cancer phenotypes and genotypes and thus be applied to cancer medicine.
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Affiliation(s)
- Yangyang Wang
- School of Electronics and Information, Northwestern Polytechnical University, Xi'an 710129, China
| | - Xiaoguang Gao
- School of Electronics and Information, Northwestern Polytechnical University, Xi'an 710129, China
| | - Jihan Wang
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an 710072, China
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12
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Romano A, Rižner TL, Werner HMJ, Semczuk A, Lowy C, Schröder C, Griesbeck A, Adamski J, Fishman D, Tokarz J. Endometrial cancer diagnostic and prognostic algorithms based on proteomics, metabolomics, and clinical data: a systematic review. Front Oncol 2023; 13:1120178. [PMID: 37091170 PMCID: PMC10118013 DOI: 10.3389/fonc.2023.1120178] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/06/2023] [Indexed: 04/09/2023] Open
Abstract
Endometrial cancer is the most common gynaecological malignancy in developed countries. Over 382,000 new cases were diagnosed worldwide in 2018, and its incidence and mortality are constantly rising due to longer life expectancy and life style factors including obesity. Two major improvements are needed in the management of patients with endometrial cancer, i.e., the development of non/minimally invasive tools for diagnostics and prognostics, which are currently missing. Diagnostic tools are needed to manage the increasing number of women at risk of developing the disease. Prognostic tools are necessary to stratify patients according to their risk of recurrence pre-preoperatively, to advise and plan the most appropriate treatment and avoid over/under-treatment. Biomarkers derived from proteomics and metabolomics, especially when derived from non/minimally-invasively collected body fluids, can serve to develop such prognostic and diagnostic tools, and the purpose of the present review is to explore the current research in this topic. We first provide a brief description of the technologies, the computational pipelines for data analyses and then we provide a systematic review of all published studies using proteomics and/or metabolomics for diagnostic and prognostic biomarker discovery in endometrial cancer. Finally, conclusions and recommendations for future studies are also given.
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Affiliation(s)
- Andrea Romano
- Department of Gynaecology, Maastricht University Medical Centre (MUMC), Maastricht, Netherlands
- GROW – School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
- *Correspondence: Andrea Romano, ; Tea Lanišnik Rižner,
| | - Tea Lanišnik Rižner
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- *Correspondence: Andrea Romano, ; Tea Lanišnik Rižner,
| | - Henrica Maria Johanna Werner
- Department of Gynaecology, Maastricht University Medical Centre (MUMC), Maastricht, Netherlands
- GROW – School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
| | - Andrzej Semczuk
- Department of Gynaecology, Lublin Medical University, Lublin, Poland
| | | | | | | | - Jerzy Adamski
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Dmytro Fishman
- Institute of Computer Science, University of Tartu, Tartu, Estonia
- Quretec Ltd., Tartu, Estonia
| | - Janina Tokarz
- Institute for Diabetes and Cancer, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
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13
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Shen Y, Wang X, Ni Z, Xu S, Qiu S, Zheng W, Zhang J. Identification of acetyl-CoA carboxylase alpha as a prognostic and targeted candidate for hepatocellular carcinoma. Clin Transl Oncol 2023:10.1007/s12094-023-03137-1. [PMID: 36976490 DOI: 10.1007/s12094-023-03137-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/26/2023] [Indexed: 03/29/2023]
Abstract
PURPOSE The de novo lipogenesis has been a longstanding observation in hepatocellular carcinoma (HCC). However, the prognostic value and carcinogenic roles of the enzyme Acetyl-CoA carboxylase alpha (ACACA) in HCC remains unknown. METHODS The proteins with remarkable prognostic significance were screened out from The Cancer Proteome Atlas Portal (TCPA) database. Furthermore, the expression characteristics and prognostic value of ACACA were evaluated in multiple databases and the local HCC cohort. The loss-of-function assays were performed to uncover the potential roles of ACACA in steering malignant behaviors of HCC cells. The underlying mechanisms were conjectured by bioinformatics and validated in HCC cell lines. RESULTS ACACA was identified as a crucial factor of HCC prognosis. Bioinformatics analyses showed that HCC patients with higher expression of ACACA protein or mRNA levels had poor prognosis. Knockdown of ACACA remarkably crippled the proliferation, colony formation, migration, invasion, epithelial-mesenchymal transition (EMT) process of HCC cells and induced the cell cycle arrest. Mechanistically, ACACA might facilitate the malignant phenotypes of HCC through aberrant activation of Wnt/β-catenin signaling pathway. In addition, ACACA expression was associated with the dilute infiltration of immune cells including plasmacytoid DC (pDC) and cytotoxic cells by utilization of relevant database analysis. CONCLUSION ACACA could be a potential biomarker and molecular target for HCC.
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Affiliation(s)
- Yiping Shen
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Xin Wang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
- Department of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Zhiyu Ni
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Shiyu Xu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Shi Qiu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
- Department of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Wenjie Zheng
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China.
- Department of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China.
| | - Jie Zhang
- Department of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China.
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14
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Xiong Z, Xing C, Zhang P, Diao Y, Guang C, Ying Y, Zhang W. Identification of a Novel Protein-Based Prognostic Model in Gastric Cancers. Biomedicines 2023; 11:biomedicines11030983. [PMID: 36979962 PMCID: PMC10046574 DOI: 10.3390/biomedicines11030983] [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: 12/18/2022] [Revised: 02/14/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
Gastric cancer (GC) is the third leading cause of cancer-related deaths worldwide. However, there are still no reliable biomarkers for the prognosis of this disease. This study aims to construct a robust protein-based prognostic prediction model for GC patients. The protein expression data and clinical information of GC patients were downloaded from the TCPA and TCGA databases, and the expressions of 218 proteins in 352 GC patients were analyzed using bioinformatics methods. Additionally, Kaplan-Meier (KM) survival analysis and univariate and multivariate Cox regression analysis were applied to screen the prognosis-related proteins for establishing the prognostic prediction risk model. Finally, five proteins, including NDRG1_pT346, SYK, P90RSK, TIGAR, and XBP1, were related to the risk prognosis of gastric cancer and were selected for model construction. Furthermore, a significant trend toward worse survival was found in the high-risk group (p = 1.495 × 10-7). The time-dependent ROC analysis indicated that the model had better specificity and sensitivity compared to the clinical features at 1, 2, and 3 years (AUC = 0.685, 0.673, and 0.665, respectively). Notably, the independent prognostic analysis results revealed that the model was an independent prognostic factor for GC patients. In conclusion, the robust protein-based model based on five proteins was established, and its potential benefits in the prognostic prediction of GC patients were demonstrated.
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Affiliation(s)
- Zhijuan Xiong
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
- Jiangxi Medical Center for Major Public Health Events, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
- The Department of Respiratory and Intensive Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Chutian Xing
- Queen Mary School, Nanchang University, Nanchang 330006, China
| | - Ping Zhang
- The Department of Respiratory and Intensive Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Yunlian Diao
- The Department of Respiratory and Intensive Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Chenxi Guang
- Jiangxi Medical Center for Major Public Health Events, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Ying Ying
- Jiangxi Medical Center for Major Public Health Events, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Wei Zhang
- Jiangxi Medical Center for Major Public Health Events, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
- The Department of Respiratory and Intensive Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
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15
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Comprehensive analysis of novel prognosis-related proteomic signature effectively improve risk stratification and precision treatment for patients with cervical cancer. Arch Gynecol Obstet 2023; 307:903-917. [PMID: 35713693 DOI: 10.1007/s00404-022-06642-w] [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: 03/13/2021] [Accepted: 05/17/2022] [Indexed: 11/02/2022]
Abstract
OBJECTIVE Cervical cancer (CC) is one of the most common types of malignant female cancer, and its incidence and mortality are not optimistic. Protein panels can be a powerful prognostic factor for many types of cancer. The purpose of our study was to investigate a proteomic panel to predict the survival of patients with common CC. METHODS AND RESULTS The protein expression and clinicopathological data of CC were downloaded from The Cancer Proteome Atlas and The Cancer Genome Atlas database, respectively. We selected the prognosis-related proteins (PRPs) by univariate Cox regression analysis and found that the results of functional enrichment analysis were mainly related to apoptosis. We used Kaplan-Meier analysis and multivariable Cox regression analysis further to screen PRPs to establish a prognostic model, including BCL2, SMAD3, and 4EBP1-pT70. The signature was verified to be independent predictors of OS by Cox regression analysis and the area under curves. Nomogram and subgroup classification were established based on the signature to verify its clinical application. Furthermore, we looked for the co-expressed proteins of three-protein panel as potential prognostic proteins. CONCLUSION A proteomic signature independently predicted OS of CC patients, and the predictive ability was better than the clinicopathological characteristics. This signature can help improve prediction for clinical outcome and provides new targets for CC treatment.
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16
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OSppc: A web server for online survival analysis using proteome of pan-cancers. J Proteomics 2023; 273:104810. [PMID: 36587732 DOI: 10.1016/j.jprot.2022.104810] [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: 04/21/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022]
Abstract
Prognostic biomarker, as a feasible and objective indicator, is valuable in the assessment of cancer risk. With the development of high-throughput sequencing technology, the screening of prognostic biomarkers has become easy, but it is difficult to screen prognostic markers based on proteomic data. In this study we developed a tool named Online consensus Survival analysis web server based on Proteome of Pan-cancers, abbreviated as OSppc, to evaluate the prognostic values of protein biomarkers. >8000 cancer cases with proteomic data, transcriptomic data and clinical follow-up information were collected from TCGA and CPTAC. 14,038 proteins (including proteins and their phosphorylated forms) analyzed by reverse-phase protein arrays and mass spectrometry in 33 types of cancers were collected. In OSppc, three analysis modules are provided, including Survival Analysis, Differential Analysis and Correlation Analysis. Survival analysis module exhibits HR with 95% CI and KM curves with log-rank p value of protein and mRNA levels of input genes. Differential analysis module shows the box plots of protein expression levels in different tissues. Correlation analysis module provides scatter plot with pearson's and spearman's correlation coefficient of the protein and its corresponding mRNA. OSppc can be accessed at http://bioinfo.henu.edu.cn/Protein/OSppc.html. SIGNIFICANCE: OSppc can analyze the association between protein, mRNA and prognosis, the correlation between proteome data and gene expression profiles, the differential expression of proteome data between subgroups such as normal and cancer as well. OSppc is registration-free and very valuable to evaluate the prognostic potency of protein of interests. OSppc is very valuable for researchers and clinicians to screen, develop and validate potential protein prognostic biomarkers in pan-cancers, and offers the opportunities to investigate the clinical important functional genes and therapeutic targets of cancers.
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17
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Shah SD, Nayak AP, Sharma P, Villalba DR, Addya S, Huang W, Shapiro P, Kane MA, Deshpande DA. Targeted Inhibition of Select Extracellular Signal-regulated Kinases 1 and 2 Functions Mitigates Pathological Features of Asthma in Mice. Am J Respir Cell Mol Biol 2023; 68:23-38. [PMID: 36067041 PMCID: PMC9817918 DOI: 10.1165/rcmb.2022-0110oc] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/26/2022] [Indexed: 02/05/2023] Open
Abstract
ERK1/2 (extracellular signal-regulated kinases 1 and 2) regulate the activity of various transcription factors that contribute to asthma pathogenesis. Although an attractive drug target, broadly inhibiting ERK1/2 is challenging because of unwanted cellular toxicities. We have identified small molecule inhibitors with a benzenesulfonate scaffold that selectively inhibit ERK1/2-mediated activation of AP-1 (activator protein-1). Herein, we describe the findings of targeting ERK1/2-mediated substrate-specific signaling with the small molecule inhibitor SF-3-030 in a murine model of house dust mite (HDM)-induced asthma. In 8- to 10-week-old BALB/c mice, allergic asthma was established by repeated intranasal HDM (25 μg/mouse) instillation for 3 weeks (5 days/week). A subgroup of mice was prophylactically dosed with 10 mg/kg SF-3-030/DMSO intranasally 30 minutes before the HDM challenge. Following the dosing schedule, mice were evaluated for alterations in airway mechanics, inflammation, and markers of airway remodeling. SF-3-030 treatment significantly attenuated HDM-induced elevation of distinct inflammatory cell types and cytokine concentrations in BAL and IgE concentrations in the lungs. Histopathological analysis of lung tissue sections revealed diminished HDM-induced pleocellular peribronchial inflammation, mucus cell metaplasia, collagen accumulation, thickening of airway smooth muscle mass, and expression of markers of cell proliferation (Ki-67 and cyclin D1) in mice treated with SF-3-030. Furthermore, SF-3-030 treatment attenuated HDM-induced airway hyperresponsiveness in mice. Finally, mechanistic studies using transcriptome and proteome analyses suggest inhibition of HDM-induced genes involved in inflammation, cell proliferation, and tissue remodeling by SF-3-030. These preclinical findings demonstrate that function-selective inhibition of ERK1/2 signaling mitigates multiple features of asthma in a murine model.
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Affiliation(s)
- Sushrut D. Shah
- Center for Translational Medicine, Jane and Leonard Korman Lung Center, and
| | - Ajay P. Nayak
- Center for Translational Medicine, Jane and Leonard Korman Lung Center, and
| | - Pawan Sharma
- Center for Translational Medicine, Jane and Leonard Korman Lung Center, and
| | | | - Sankar Addya
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania; and
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland
| | - Paul Shapiro
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland
| | - Maureen A. Kane
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland
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18
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Kossinna P, Cai W, Lu X, Shemanko CS, Zhang Q. Stabilized COre gene and Pathway Election uncovers pan-cancer shared pathways and a cancer-specific driver. SCIENCE ADVANCES 2022; 8:eabo2846. [PMID: 36542714 PMCID: PMC9770999 DOI: 10.1126/sciadv.abo2846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Approaches systematically characterizing interactions via transcriptomic data usually follow two systems: (i) coexpression network analyses focusing on correlations between genes and (ii) linear regressions (usually regularized) to select multiple genes jointly. Both suffer from the problem of stability: A slight change of parameterization or dataset could lead to marked alterations of outcomes. Here, we propose Stabilized COre gene and Pathway Election (SCOPE), a tool integrating bootstrapped least absolute shrinkage and selection operator and coexpression analysis, leading to robust outcomes insensitive to variations in data. By applying SCOPE to six cancer expression datasets (BRCA, COAD, KIRC, LUAD, PRAD, and THCA) in The Cancer Genome Atlas, we identified core genes capturing interaction effects in crucial pan-cancer pathways related to genome instability and DNA damage response. Moreover, we highlighted the pivotal role of CD63 as an oncogenic driver and a potential therapeutic target in kidney cancer. SCOPE enables stabilized investigations toward complex interactions using transcriptome data.
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Affiliation(s)
- Pathum Kossinna
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta T2N 1N4, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Weijia Cai
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Xuewen Lu
- Department of Mathematics and Statistics, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Carrie S. Shemanko
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
- Arnie Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Qingrun Zhang
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta T2N 1N4, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 1N4, Canada
- Department of Mathematics and Statistics, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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Tiong KL, Sintupisut N, Lin MC, Cheng CH, Woolston A, Lin CH, Ho M, Lin YW, Padakanti S, Yeang CH. An integrated analysis of the cancer genome atlas data discovers a hierarchical association structure across thirty three cancer types. PLOS DIGITAL HEALTH 2022; 1:e0000151. [PMID: 36812605 PMCID: PMC9931374 DOI: 10.1371/journal.pdig.0000151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 10/31/2022] [Indexed: 06/18/2023]
Abstract
Cancer cells harbor molecular alterations at all levels of information processing. Genomic/epigenomic and transcriptomic alterations are inter-related between genes, within and across cancer types and may affect clinical phenotypes. Despite the abundant prior studies of integrating cancer multi-omics data, none of them organizes these associations in a hierarchical structure and validates the discoveries in extensive external data. We infer this Integrated Hierarchical Association Structure (IHAS) from the complete data of The Cancer Genome Atlas (TCGA) and compile a compendium of cancer multi-omics associations. Intriguingly, diverse alterations on genomes/epigenomes from multiple cancer types impact transcriptions of 18 Gene Groups. Half of them are further reduced to three Meta Gene Groups enriched with (1) immune and inflammatory responses, (2) embryonic development and neurogenesis, (3) cell cycle process and DNA repair. Over 80% of the clinical/molecular phenotypes reported in TCGA are aligned with the combinatorial expressions of Meta Gene Groups, Gene Groups, and other IHAS subunits. Furthermore, IHAS derived from TCGA is validated in more than 300 external datasets including multi-omics measurements and cellular responses upon drug treatments and gene perturbations in tumors, cancer cell lines, and normal tissues. To sum up, IHAS stratifies patients in terms of molecular signatures of its subunits, selects targeted genes or drugs for precision cancer therapy, and demonstrates that associations between survival times and transcriptional biomarkers may vary with cancer types. These rich information is critical for diagnosis and treatments of cancers.
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Affiliation(s)
- Khong-Loon Tiong
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
| | - Nardnisa Sintupisut
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
| | - Min-Chin Lin
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
- Psomagen, Rockville, Maryland, United States of America
| | - Chih-Hung Cheng
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
| | - Andrew Woolston
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
- Translational Cancer Immunotherapy & Genomics Lab, Barts Cancer Institute, Charterhouse Square, London, United Kingdom
| | - Chih-Hsu Lin
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
- C3.ai, Redwood City, California, United States of America
| | - Mirrian Ho
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
| | - Yu-Wei Lin
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
- AiLife Diagnostics, Pearland, Texas, United States of America
| | - Sridevi Padakanti
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
| | - Chen-Hsiang Yeang
- Institute of Statistical Science, Academia Sinica, Section 2, Taipei, Taiwan
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20
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Zhang J, Pan T, Zhou W, Zhang Y, Xu G, Xu Q, Li S, Gao Y, Wang Z, Xu J, Li Y. Long noncoding RNA LINC01132 enhances immunosuppression and therapy resistance via NRF1/DPP4 axis in hepatocellular carcinoma. J Exp Clin Cancer Res 2022; 41:270. [PMID: 36071454 PMCID: PMC9454129 DOI: 10.1186/s13046-022-02478-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/28/2022] [Indexed: 12/21/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) are emerging as critical regulators of gene expression and play fundamental roles in various types of cancer. Current developments in transcriptome analyses unveiled the existence of lncRNAs; however, their functional characterization remains a challenge. Methods A bioinformatics screen was performed by integration of multiple omics data in hepatocellular carcinoma (HCC) prioritizing a novel oncogenic lncRNA, LINC01132. Expression of LINC01132 in HCC and control tissues was validated by qRT-PCR. Cell viability and migration activity was examined by MTT and transwell assays. Finally, our results were confirmed in vivo mouse model and ex vivo patient derived tumor xenograft experiments to determine the mechanism of action and explore LINC01132-targeted immunotherapy. Results Systematic investigation of lncRNAs genome-wide expression patterns revealed LINC01132 as an oncogene in HCC. LINC01132 is significantly overexpressed in tumor and associated with poor overall survival of HCC patients, which is mainly driven by copy number amplification. Functionally, LINC01132 overexpression promoted cell growth, proliferation, invasion and metastasis in vitro and in vivo. Mechanistically, LINC01132 acts as an oncogenic driver by physically interacting with NRF and enhancing the expression of DPP4. Notably, LINC01132 silencing triggers CD8+ T cells infiltration, and LINC01132 knockdown combined with anti-PDL1 treatment improves antitumor immunity, which may prove a new combination therapy in HCC. Conclusions LINC01132 functions as an oncogenic driver that induces HCC development via the NRF1/DPP4 axis. Silencing LINC01132 may enhance the efficacy of anti-PDL1 immunotherapy in HCC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02478-z.
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The Prediction of a 3-Protein-Based Model on the Prognosis of Head and Neck Squamous Cell Carcinoma. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:2161122. [PMID: 35756403 PMCID: PMC9232309 DOI: 10.1155/2022/2161122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/23/2022] [Accepted: 05/28/2022] [Indexed: 12/24/2022]
Abstract
Background Head and neck squamous cell carcinoma (HNSCC) is one of the commonest malignant tumors. Using high-throughput genomic methods, RNA-based diagnostic and prognostic models for HNSCC with potential clinical value have been developed. However, the clinical utility and reproducibility of these models are uncertain. Because the complex regulatory processes occurring after mRNA is transcribed, the abundance of proteins in a cell can never be fully predicted or explained by their corresponding mRNA expression. We aimed to assume and verify a novel protein signature for checking the HNSCC patients' prognosis. Methods The functional proteomic data of 332 HNSCC cases were collected from The Cancer Proteome Atlas (TCPA), and the related follow-up and clinical data were acquired from The Cancer Genome Atlas (TCGA). This study adopted multivariate and univariate Cox regression analysis, Akaike Information Criterion, receiver operating characteristic (ROC) analysis, and Kaplan-Meier method. Results Patients' clinical features in both sets were comparable (all, P > 0.05). The area under the ROC curve (AUC) for the 3-protein signature (X4EBP1_pT37T46, HER3_pY1289, and NF2) in the test set was 0.655 and in the combined cohort (all 332 patients combined) was 0.699. In addition, the 3-protein signature exhibited better predictive value for the survival of HNSCC patients as in comparison with conventional clinical factors like age, gender, tumor stage, and smoking history (TNM stage). Conclusion The 3-protein signature developed in this study exhibits good performance in predicting the overall survival of with HNSCC patients. The 3-protein signature exhibited better predictive value for survival than conventional clinical factors just like gender, TNM stage, smoking history, and age.
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22
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Deciphering specific miRNAs in brain tumors: a 5-miRNA signature in glioblastoma. Mol Genet Genomics 2022; 297:507-521. [PMID: 35175428 DOI: 10.1007/s00438-022-01866-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/26/2022] [Indexed: 12/20/2022]
Abstract
MicroRNAs are endogenous non-coding RNAs with a marked impact on the development and progression of brain tumors. However, they commonly share different expression patterns in other types of tumors, thereby exhibiting lack of tissue specificity. Here, an integrative holistic analysis of microarray data is established for deciphering dysregulated miRNAs in glioblastoma, distinguishing them from eight other CNS tumors. The identification of dysregulated miRNAs was performed in a pool of 176 patients, 118 of which diagnosed with glioblastoma. Dysregulated miRNAs commonly expressed in glioblastoma were then discriminated from those co-expressed in other CNS tumors and further characterized. Overall, 21 miRNAs were found to be commonly dysregulated in glioblastoma. Notwithstanding, 16 miRNAs also exhibited a differential expression in at least one other CNS tumor. The remaining 5, specifically, hsa-miR-21-3p, hsa-miR-338-5p, hsa-miR-485-5p, hsa-miR-491-5p and hsa-miR-1290, were solely associated to glioblastoma. This signature is in-depth characterized, with the spotlight on tumor progression, invasion and patient survival. These five endogenous molecules, differentially expressed in glioblastoma, are thus suggested as potential therapeutic targets, modulating several genes involved in major signalling pathways, including MAPK/ERK, calcium, PI3K/AKT, mTOR and Wnt. In summary, these findings lay a foundation for further research on the expression and function of specific patterns of miRNAs expression in glioblastoma, providing reference for potential novel targets.
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23
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Johnson BE, Creason AL, Stommel JM, Keck JM, Parmar S, Betts CB, Blucher A, Boniface C, Bucher E, Burlingame E, Camp T, Chin K, Eng J, Estabrook J, Feiler HS, Heskett MB, Hu Z, Kolodzie A, Kong BL, Labrie M, Lee J, Leyshock P, Mitri S, Patterson J, Riesterer JL, Sivagnanam S, Somers J, Sudar D, Thibault G, Weeder BR, Zheng C, Nan X, Thompson RF, Heiser LM, Spellman PT, Thomas G, Demir E, Chang YH, Coussens LM, Guimaraes AR, Corless C, Goecks J, Bergan R, Mitri Z, Mills GB, Gray JW. An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer. Cell Rep Med 2022; 3:100525. [PMID: 35243422 PMCID: PMC8861971 DOI: 10.1016/j.xcrm.2022.100525] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/15/2021] [Accepted: 01/19/2022] [Indexed: 12/15/2022]
Abstract
Mechanisms of therapeutic resistance and vulnerability evolve in metastatic cancers as tumor cells and extrinsic microenvironmental influences change during treatment. To support the development of methods for identifying these mechanisms in individual people, here we present an omic and multidimensional spatial (OMS) atlas generated from four serial biopsies of an individual with metastatic breast cancer during 3.5 years of therapy. This resource links detailed, longitudinal clinical metadata that includes treatment times and doses, anatomic imaging, and blood-based response measurements to clinical and exploratory analyses, which includes comprehensive DNA, RNA, and protein profiles; images of multiplexed immunostaining; and 2- and 3-dimensional scanning electron micrographs. These data report aspects of heterogeneity and evolution of the cancer genome, signaling pathways, immune microenvironment, cellular composition and organization, and ultrastructure. We present illustrative examples of how integrative analyses of these data reveal potential mechanisms of response and resistance and suggest novel therapeutic vulnerabilities.
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Affiliation(s)
- Brett E. Johnson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Allison L. Creason
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jayne M. Stommel
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jamie M. Keck
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Swapnil Parmar
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Courtney B. Betts
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Aurora Blucher
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Christopher Boniface
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Elmar Bucher
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Erik Burlingame
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Todd Camp
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Koei Chin
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jennifer Eng
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Joseph Estabrook
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Heidi S. Feiler
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Michael B. Heskett
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Zhi Hu
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Annette Kolodzie
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ben L. Kong
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Pharmacy Services, Oregon Health & Science University, Portland, OR 97239, USA
| | - Marilyne Labrie
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jinho Lee
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Patrick Leyshock
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Souraya Mitri
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Janice Patterson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jessica L. Riesterer
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Multiscale Microscopy Core, Oregon Health & Science University, Portland, OR 97239, USA
| | - Shamilene Sivagnanam
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Julia Somers
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Damir Sudar
- Quantitative Imaging Systems LLC, Portland, OR 97239, USA
| | - Guillaume Thibault
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Benjamin R. Weeder
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Christina Zheng
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Xiaolin Nan
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Reid F. Thompson
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Hospital and Specialty Medicine, VA Portland Healthcare System, Portland, OR 97239, USA
| | - Laura M. Heiser
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Paul T. Spellman
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - George Thomas
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Pathology & Laboratory Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Emek Demir
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Young Hwan Chang
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Lisa M. Coussens
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Alexander R. Guimaraes
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Diagnostic Radiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Christopher Corless
- Department of Pharmacy Services, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Pathology & Laboratory Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jeremy Goecks
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Raymond Bergan
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Zahi Mitri
- Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Medicine, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Gordon B. Mills
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Joe W. Gray
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
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24
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Huang L, Zhu H, Luo Z, Luo C, Luo L, Nong B, Zhang S, Wan C, Wang Y, Songyang Z, Xiong Y. FPIA: A database for gene fusion profiling and interactive analyses. Int J Cancer 2022; 150:1504-1511. [PMID: 34985769 DOI: 10.1002/ijc.33921] [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: 08/06/2021] [Revised: 12/05/2021] [Accepted: 12/16/2021] [Indexed: 11/09/2022]
Abstract
As one of the hallmarks of cancer, gene fusions play an important role in tumorigenesis, and have been established as biomarkers and therapeutic targets. Although recent years have witnessed the development of gene fusion databases, a tool with interactive analytic functions is still lacking. Here, we introduce FPIA (Fusion Profiling Interactive Analysis), a web server to perform interactive and customizable analysis on fusion genes. With this platform, researchers can easily explore fusion-associated biological and molecular differences including gene expression, tumor purity and ploidy, mutation, copy number variations, protein expression, immune cell infiltration, stemness, telomere length, microsatellite instability, survival, and novel peptides based on 33 cancer types from TCGA data. Currently, it contains 31 633 fusion events from 6910 patients. FPIA complements the existing gene fusion annotation databases with its multi-omics analytic capacity, integrated analysis features, customized analysis selection, and user-friendly design. The comprehensive data analyses by FPIA will greatly facilitate data mining, hypothesis generation, and therapeutic target discovery. FPIA is available at http://bioinfo-sysu.com/fpia.
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Affiliation(s)
- Lu Huang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Huiming Zhu
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhenhua Luo
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Chukun Luo
- School of Automation, Guangdong University of Technology, Guangzhou, China
| | - Linjiang Luo
- School of Automation, Guangdong University of Technology, Guangzhou, China
| | - Baoting Nong
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Shiyu Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Chengcheng Wan
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yanzhi Wang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Zhou Songyang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, USA
| | - Yuanyan Xiong
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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25
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Wei Z, Sijia F, Rui T, Yang L, Jianjun H, Bin W, Jing X. Analysis of differentially expressed proteins between HER2 positive and triple negative breast cancer and their prognostic significance. Ann Diagn Pathol 2021; 55:151834. [PMID: 34610510 DOI: 10.1016/j.anndiagpath.2021.151834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 09/19/2021] [Indexed: 01/08/2023]
Abstract
Both triple negative breast cancer (TNBA) and HER2-positive breast cancer lack expression of estrogen receptor alpha (ER) and progesterone receptor (PR), while human epidermal growth factor receptor 2 (HER2) in TNBC is also negative. This study aimed to identify the differentially expressed proteins (DEPs) between TNBC and HER2-positive breast cancer and to improve understanding of their role in the prognosis of breast cancer. By analyzing the breast cancer data set in The Cancer Proteome Atlas (TCPA) database, 15 DEPs between TNBC and HER2-positive breast cancer were identified. GO and pathway enrichment analysis were performed on DEPs, and the protein-protein interaction (PPI) network was constructed. The overall survival (OS) analysis of the breast cancer protein dataset in the Kaplan-Meier plotter showed that low expression of ACC1 suggested a higher OS of HER2-positive breast cancer (HR = 5.34, P < 0.05) and TNBC (HR = 2.88, P < 0.05). And TNBC patients with high TBA1B (HR = 0.16, P < 0.01) or low INPP4B (HR = 3.47, P < 0.05) expression have a better prognosis. Our research provides new insights into the prognostic indicators of TNBC and HER2-positive breast cancer, which could be further studied.
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Affiliation(s)
- Zhang Wei
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China.
| | - Fei Sijia
- Department of Geriatric Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Tong Rui
- Department of Geriatric Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Liu Yang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - He Jianjun
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Wan Bin
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Xu Jing
- Department of Geriatric Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China.
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26
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Drug-Induced Resistance and Phenotypic Switch in Triple-Negative Breast Cancer Can Be Controlled via Resolution and Targeting of Individualized Signaling Signatures. Cancers (Basel) 2021; 13:cancers13195009. [PMID: 34638492 PMCID: PMC8507629 DOI: 10.3390/cancers13195009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 09/29/2021] [Indexed: 12/28/2022] Open
Abstract
Simple Summary Patients with Triple Negative Breast Cancer (TNBC) have a poor prognosis due to high inter-tumor heterogeneity and absence of effective targeted treatments. Through quantification of ongoing processes in each individual with TNBC, we propose an explanation on why certain previously suggested monotherapies, such as anti-EGFR, are not effective. We experimentally demonstrate that monotherapies or drug combinations that are not adjusted accurately to the patient-specific ongoing processes may create an evolutionary pressure on a tumor leading to the emergence of previously undetected or untargeted cellular subpopulations. We show for example that certain TNBC tumors may benefit from therapies targeting estrogen receptors (ER), similarly to ER positive cancers. When untargeted, those tumors may develop large ER positive subpopulations. We propose that anti-TNBC therapy should be accurately tailored to the personalized molecular processes and that incomplete or “wrong” treatments may generate diverse evolutionary routes of TNBC tumors leading to drug resistance. Abstract Triple-negative breast cancer (TNBC) is an aggressive subgroup of breast cancers which is treated mainly with chemotherapy and radiotherapy. Epidermal growth factor receptor (EGFR) was considered to be frequently expressed in TNBC, and therefore was suggested as a therapeutic target. However, clinical trials of EGFR inhibitors have failed. In this study, we examine the relationship between the patient-specific TNBC network structures and possible mechanisms of resistance to anti-EGFR therapy. Using an information-theoretical analysis of 747 breast tumors from the TCGA dataset, we resolved individualized protein network structures, namely patient-specific signaling signatures (PaSSS) for each tumor. Each PaSSS was characterized by a set of 1–4 altered protein–protein subnetworks. Thirty-one percent of TNBC PaSSSs were found to harbor EGFR as a part of the network and were predicted to benefit from anti-EGFR therapy as long as it is combined with anti-estrogen receptor (ER) therapy. Using a series of single-cell experiments, followed by in vivo support, we show that drug combinations which are not tailored accurately to each PaSSS may generate evolutionary pressure in malignancies leading to an expansion of the previously undetected or untargeted subpopulations, such as ER+ populations. This corresponds to the PaSSS-based predictions suggesting to incorporate anti-ER drugs in certain anti-TNBC treatments. These findings highlight the need to tailor anti-TNBC targeted therapy to each PaSSS to prevent diverse evolutions of TNBC tumors and drug resistance development.
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27
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Vitorino R, Choudhury M, Guedes S, Ferreira R, Thongboonkerd V, Sharma L, Amado F, Srivastava S. Peptidomics and proteogenomics: background, challenges and future needs. Expert Rev Proteomics 2021; 18:643-659. [PMID: 34517741 DOI: 10.1080/14789450.2021.1980388] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION With available genomic data and related information, it is becoming possible to better highlight mutations or genomic alterations associated with a particular disease or disorder. The advent of high-throughput sequencing technologies has greatly advanced diagnostics, prognostics, and drug development. AREAS COVERED Peptidomics and proteogenomics are the two post-genomic technologies that enable the simultaneous study of peptides and proteins/transcripts/genes. Both technologies add a remarkably large amount of data to the pool of information on various peptides associated with gene mutations or genome remodeling. Literature search was performed in the PubMed database and is up to date. EXPERT OPINION This article lists various techniques used for peptidomic and proteogenomic analyses. It also explains various bioinformatics workflows developed to understand differentially expressed peptides/proteins and their role in disease pathogenesis. Their role in deciphering disease pathways, cancer research, and biomarker discovery using biofluids is highlighted. Finally, the challenges and future requirements to overcome the current limitations for their effective clinical use are also discussed.
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Affiliation(s)
- Rui Vitorino
- Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.,Laqv/requimte, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Manisha Choudhury
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Powai, India
| | - Sofia Guedes
- Laqv/requimte, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Rita Ferreira
- Laqv/requimte, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Francisco Amado
- Laqv/requimte, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Powai, India
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28
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Chi LH, Wu ATH, Hsiao M, Li YC(J. A Transcriptomic Analysis of Head and Neck Squamous Cell Carcinomas for Prognostic Indications. J Pers Med 2021; 11:782. [PMID: 34442426 PMCID: PMC8399099 DOI: 10.3390/jpm11080782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 01/27/2023] Open
Abstract
Survival analysis of the Cancer Genome Atlas (TCGA) dataset is a well-known method for discovering gene expression-based prognostic biomarkers of head and neck squamous cell carcinoma (HNSCC). A cutoff point is usually used in survival analysis for patient dichotomization when using continuous gene expression values. There is some optimization software for cutoff determination. However, the software's predetermined cutoffs are usually set at the medians or quantiles of gene expression values. There are also few clinicopathological features available in pre-processed datasets. We applied an in-house workflow, including data retrieving and pre-processing, feature selection, sliding-window cutoff selection, Kaplan-Meier survival analysis, and Cox proportional hazard modeling for biomarker discovery. In our approach for the TCGA HNSCC cohort, we scanned human protein-coding genes to find optimal cutoff values. After adjustments with confounders, clinical tumor stage and surgical margin involvement were found to be independent risk factors for prognosis. According to the results tables that show hazard ratios with Bonferroni-adjusted p values under the optimal cutoff, three biomarker candidates, CAMK2N1, CALML5, and FCGBP, are significantly associated with overall survival. We validated this discovery by using the another independent HNSCC dataset (GSE65858). Thus, we suggest that transcriptomic analysis could help with biomarker discovery. Moreover, the robustness of the biomarkers we identified should be ensured through several additional tests with independent datasets.
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Affiliation(s)
- Li-Hsing Chi
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (L.-H.C.); (A.T.H.W.)
- Division of Oral and Maxillofacial Surgery, Department of Dentistry, Wan Fang Hospital, Taipei Medical University, Taipei 11600, Taiwan
- Division of Oral and Maxillofacial Surgery, Department of Dentistry, Taipei Medical University Hospital, Taipei Medical University, Taipei 11031, Taiwan
| | - Alexander T. H. Wu
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (L.-H.C.); (A.T.H.W.)
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei 115024, Taiwan
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
| | - Yu-Chuan (Jack) Li
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (L.-H.C.); (A.T.H.W.)
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, No.172-1, Sec. 2, Keelung Rd., Taipei 106339, Taiwan
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29
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Morgan EL, Scarth JA, Patterson MR, Wasson CW, Hemingway GC, Barba-Moreno D, Macdonald A. E6-mediated activation of JNK drives EGFR signalling to promote proliferation and viral oncoprotein expression in cervical cancer. Cell Death Differ 2021; 28:1669-1687. [PMID: 33303976 PMCID: PMC8166842 DOI: 10.1038/s41418-020-00693-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 02/06/2023] Open
Abstract
Human papillomaviruses (HPV) are a major cause of malignancy worldwide, contributing to ~5% of all human cancers including almost all cases of cervical cancer and a growing number of ano-genital and oral cancers. HPV-induced malignancy is primarily driven by the viral oncogenes, E6 and E7, which manipulate host cellular pathways to increase cell proliferation and enhance cell survival, ultimately predisposing infected cells to malignant transformation. Consequently, a more detailed understanding of viral-host interactions in HPV-associated disease offers the potential to identify novel therapeutic targets. Here, we identify that the c-Jun N-terminal kinase (JNK) signalling pathway is activated in cervical disease and in cervical cancer. The HPV E6 oncogene induces JNK1/2 phosphorylation in a manner that requires the E6 PDZ binding motif. We show that blockade of JNK1/2 signalling using small molecule inhibitors, or knockdown of the canonical JNK substrate c-Jun, reduces cell proliferation and induces apoptosis in cervical cancer cells. We further demonstrate that this phenotype is at least partially driven by JNK-dependent activation of EGFR signalling via increased expression of EGFR and the EGFR ligands EGF and HB-EGF. JNK/c-Jun signalling promoted the invasive potential of cervical cancer cells and was required for the expression of the epithelial to mesenchymal transition (EMT)-associated transcription factor Slug and the mesenchymal marker Vimentin. Furthermore, JNK/c-Jun signalling is required for the constitutive expression of HPV E6 and E7, which are essential for cervical cancer cell growth and survival. Together, these data demonstrate a positive feedback loop between the EGFR signalling pathway and HPV E6/E7 expression, identifying a regulatory mechanism in which HPV drives EGFR signalling to promote proliferation, survival and EMT. Thus, our study has identified a novel therapeutic target that may be beneficial for the treatment of cervical cancer.
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Affiliation(s)
- Ethan L. Morgan
- grid.9909.90000 0004 1936 8403School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT UK ,grid.9909.90000 0004 1936 8403Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, West Yorkshire LS2 9JT UK ,grid.94365.3d0000 0001 2297 5165Present Address: Tumor Biology Section, Head and Neck Surgery Branch, National Institute of Deafness and Other Communication Disorders, National Institute of Health, Bethesda, MD USA
| | - James A. Scarth
- grid.9909.90000 0004 1936 8403School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT UK ,grid.9909.90000 0004 1936 8403Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, West Yorkshire LS2 9JT UK
| | - Molly R. Patterson
- grid.9909.90000 0004 1936 8403School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT UK ,grid.9909.90000 0004 1936 8403Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, West Yorkshire LS2 9JT UK
| | - Christopher W. Wasson
- grid.9909.90000 0004 1936 8403School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT UK ,grid.9909.90000 0004 1936 8403Present Address: Leeds Institute of Rheumatic and Musculoskeletal Medicine, School of Medicine, University of Leeds, St-James University Teaching Hospital, Leeds, West Yorkshire UK
| | - Georgia C. Hemingway
- grid.9909.90000 0004 1936 8403School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT UK
| | - Diego Barba-Moreno
- grid.9909.90000 0004 1936 8403School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT UK ,grid.9909.90000 0004 1936 8403Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, West Yorkshire LS2 9JT UK
| | - Andrew Macdonald
- grid.9909.90000 0004 1936 8403School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT UK ,grid.9909.90000 0004 1936 8403Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, West Yorkshire LS2 9JT UK
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Wen H, Shi W, Ge S, Li J, Zuo L, Liu M. [Value of prediction models for prognosis prediction of colorectal cancer: an analysis based on TCPA database]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:439-446. [PMID: 33849837 DOI: 10.12122/j.issn.1673-4254.2021.03.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To assess the value of the combination of multiple proteins in predicting the prognosis of colorectal cancer (CRC) through bioinformatics analysis. OBJECTIVE The protein expression and clinical data were downloaded from TCPA database. Perl and R were used to screen the prognostic-related proteins, and through Cox analysis, the proteins that served as independent prognostic factors of CRC were identified to build the prediction model. Survival analyses were conducted for each of the proteins included in the prediction model and the risk score of the model, and risk curves was drawn for the risk score and the patients' survival status to verify the performance of the model. Independent prognosis analysis and ROC analysis were used to assess the value and advantages of the model in prognosis prediction. The interactions between the proteins included in the model and the differential expressions of the key genes related with the proteins were analyzed. OBJECTIVE Six proteins were screened for model construction. Compared with a single gene, the model showed much greater prognostic value for CRC. Independent prognostic analysis showed that the risk score of the prediction model was significantly related with the prognosis (P < 0.001), and the model could be used as an independent risk factor for prognostic assessment of the patients. ROC analysis showed that the model had good specificity and sensitivity for prognostic prediction (AUC=0.734). Protein interactions showed that BID, SLC1A5 and SRC_pY527 were significantly correlated with other proteins (P < 0.001), and SLC1A5 and SRC_pY527 had the most significant interactions with other proteins (P < 0.001). Except for those of INPP4B, the key genes related with the proteins in the prediction model had significant differential expressions at the mRNA level in CRC (P < 0.05). OBJECTIVE The prediction model constructed based on 6 proteins has good prognostic value for CRC. The proteins SLC1A5 and SRC_pY527 play key roles in the prognosis of CRC, and SRC_pY527 may regulate the occurrence and progression of CRC through the SRC/AKT/MAPK signal axis and thus may serve as a new therapeutic target of CRC.
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Affiliation(s)
- H Wen
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
| | - W Shi
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
| | - S Ge
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
| | - J Li
- Department of Laboratory Medicine, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
| | - L Zuo
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
| | - M Liu
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China
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Kaur H, Kumar R, Lathwal A, Raghava GPS. Computational resources for identification of cancer biomarkers from omics data. Brief Funct Genomics 2021; 20:213-222. [PMID: 33788922 DOI: 10.1093/bfgp/elab021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/11/2021] [Accepted: 03/08/2021] [Indexed: 12/18/2022] Open
Abstract
Cancer is one of the most prevailing, deadly and challenging diseases worldwide. The advancement in technology led to the generation of different types of omics data at each genome level that may potentially improve the current status of cancer patients. These data have tremendous applications in managing cancer effectively with improved outcome in patients. This review summarizes the various computational resources and tools housing several types of omics data related to cancer. Major categorization of resources includes-cancer-associated multiomics data repositories, visualization/analysis tools for omics data, machine learning-based diagnostic, prognostic, and predictive biomarker tools, and data analysis algorithms employing the multiomics data. The review primarily focuses on providing comprehensive information on the open-source multiomics tools and data repositories, owing to their broader applicability, economic-benefit and usability. Sections including the comparative analysis, tools applicability and possible future directions have also been discussed in detail. We hope that this information will significantly benefit the researchers and clinicians, especially those with no sound background in bioinformatics and who lack sufficient data analysis skills to interpret something from the plethora of cancer-specific data generated nowadays.
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Chu G, Xu T, Zhu G, Liu S, Niu H, Zhang M. Identification of a Novel Protein-Based Signature to Improve Prognosis Prediction in Renal Clear Cell Carcinoma. Front Mol Biosci 2021; 8:623120. [PMID: 33842538 PMCID: PMC8027127 DOI: 10.3389/fmolb.2021.623120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/08/2021] [Indexed: 12/16/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignant adult kidney cancer, and its incidence and mortality are not optimistic. It is well known that tumor-related protein markers play an important role in cancer detection, prognosis prediction, or treatment selection, such as carcinoembryonic antigen (CEA), programmed cell death 1 (PD-1), programmed cell death 1 ligand 1 (PD-L1), and cytotoxic T lymphocyte antigen 4 (CTLA-4), so a comprehensive analysis was performed in this study to explore the prognostic value of protein expression in patients with ccRCC. Materials and Methods Protein expression data were obtained from The Cancer Proteome Atlas (TCPA), and clinical information were downloaded from The Cancer Genome Atlas (TCGA). We selected 445 patients with complete information and then separated them into a training set and testing set. We performed univariate, least absolute shrinkage and selection operator (LASSO) Cox analyses to find prognosis-related proteins (PRPs) and constructed a protein signature. Then, we used stratified analysis to fully verify the prognostic significance of the prognostic-related protein signature score (PRPscore). Besides, we also explored the differences in immunotherapy response and immune cell infiltration level in high and low score groups. The consensus clustering analysis was also performed to identify potential cancer subgroups. Results From the training set, a total of 233 PRPs were selected, and a seven-protein signature was constructed, including ACC1, AR, MAPK, PDK1, PEA15, SYK, and BRAF. Based on the PRPscore, patients could be divided into two groups with significantly different overall survival rates. Univariate and multivariate Cox regression analyses proved that this signature was an independent prognostic factor for patients (P < 0.001). Moreover, the signature showed a high ability to distinguish prognostic outcomes among subgroups, and the low score group had a better prognosis (P < 0.001) and better immunotherapy response (P = 0.003) than the high score group. Conclusion We constructed a novel protein signature with robust predictive power and high clinical value. This will help to guide the disease management and individualized treatment of ccRCC patients.
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Affiliation(s)
- Guangdi Chu
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ting Xu
- Department of Geratology, The 971th Hospital of PLA Navy, Qingdao, China
| | - Guanqun Zhu
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Shuaihong Liu
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Haitao Niu
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Mingxin Zhang
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China
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Fatty Acid Synthase Confers Tamoxifen Resistance to ER+/HER2+ Breast Cancer. Cancers (Basel) 2021; 13:cancers13051132. [PMID: 33800852 PMCID: PMC7961649 DOI: 10.3390/cancers13051132] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 01/16/2023] Open
Abstract
Simple Summary Overactivation of the human epidermal growth factor receptor 2 (HER2) is one of the main drivers of tamoxifen resistance in estrogen receptor (ER)-positive breast cancer patients. Combined targeting of HER2 and ER, however, has yielded disappointing results in the clinical setting. Therefore, other potential mechanisms for tamoxifen resistance would not be overcome by solely blocking the cross-talk between ER and HER2 at the receptor(s) level. Using cell lines, animal models, and clinical data, we provide evidence to support a critical role of fatty acid synthase (FASN)—the major site for endogenous fat synthesis—in HER2-driven tamoxifen resistance. Importantly, treatment with a FASN inhibitor impeded the estrogen-like tumor-promoting effects of tamoxifen and fully restored the anti-estrogenic activity of tamoxifen in ER+/HER2-overexpressing breast cancer xenografts. We postulate FASN as a biological determinant of HER2-driven tamoxifen resistance and FASN inhibition as a novel therapeutic approach to restore tamoxifen sensitivity in endocrine-resistant breast cancer. Abstract The identification of clinically important molecular mechanisms driving endocrine resistance is a priority in estrogen receptor-positive (ER+) breast cancer. Although both genomic and non-genomic cross-talk between the ER and growth factor receptors such as human epidermal growth factor receptor 2 (HER2) has frequently been associated with both experimental and clinical endocrine therapy resistance, combined targeting of ER and HER2 has failed to improve overall survival in endocrine non-responsive disease. Herein, we questioned the role of fatty acid synthase (FASN), a lipogenic enzyme linked to HER2-driven breast cancer aggressiveness, in the development and maintenance of hormone-independent growth and resistance to anti-estrogens in ER/HER2-positive (ER+/HER2+) breast cancer. The stimulatory effects of estradiol on FASN gene promoter activity and protein expression were blunted by anti-estrogens in endocrine-responsive breast cancer cells. Conversely, an AKT/MAPK-related constitutive hyperactivation of FASN gene promoter activity was unaltered in response to estradiol in non-endocrine responsive ER+/HER2+ breast cancer cells, and could be further enhanced by tamoxifen. Pharmacological blockade with structurally and mechanistically unrelated FASN inhibitors fully impeded the strong stimulatory activity of tamoxifen on the soft-agar colony forming capacity—an in vitro metric of tumorigenicity—of ER+/HER2+ breast cancer cells. In vivo treatment with a FASN inhibitor completely prevented the agonistic tumor-promoting activity of tamoxifen and fully restored its estrogen antagonist properties against ER/HER2-positive xenograft tumors in mice. Functional cancer proteomic data from The Cancer Proteome Atlas (TCPA) revealed that the ER+/HER2+ subtype was the highest FASN protein expressor compared to basal-like, HER2-enriched, and ER+/HER2-negative breast cancer groups. FASN is a biological determinant of HER2-driven endocrine resistance in ER+ breast cancer. Next-generation, clinical-grade FASN inhibitors may be therapeutically relevant to countering resistance to tamoxifen in FASN-overexpressing ER+/HER2+ breast carcinomas.
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Development of a five-protein signature for predicting the prognosis of head and neck squamous cell carcinoma. Aging (Albany NY) 2020; 12:19740-19755. [PMID: 33049713 PMCID: PMC7732293 DOI: 10.18632/aging.104036] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 08/19/2020] [Indexed: 01/24/2023]
Abstract
Currently no reliable indicators are available for predicting the clinical outcome of head and neck squamous cell carcinoma (HNSCC). This study aimed to develop a protein-based model to improve the prognosis prediction of HNSCC. The proteome data of HNSCC cohort was downloaded from The Cancer Proteome Atlas (TCPA) portal. The TCPA HNSCC cohort was randomly divided into the discovery and validation cohort. A protein-based risk signature was developed with the discovery cohort, and then verified with the validation cohort. The prognostic value of HER3_pY1289 was further determined. We have constructed a five-protein risk signature which was strongly associated with the overall survival (OS) in the discovery cohort. Similar findings were observed in the validation cohort. The protein-based risk signature was identified as an independent prognostic factor for HNSCC. A nomogram model built on the protein-based risk signature exhibited good performance for predicting OS. Our immunohistochemistry (IHC) analysis showed that higher HER3_pY1289 staining intensity was closely associated with unfavorable prognosis of HNSCC. HER3 suppression inhibited the proliferation and invasion capacity of HNSCC cells. Collectively, we have developed a protein-based risk signature for accurately predicting the prognosis of HNSCC, which might provide valuable information for optimal individualized treatment regimens.
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Mantini G, Pham TV, Piersma SR, Jimenez CR. Computational Analysis of Phosphoproteomics Data in Multi-Omics Cancer Studies. Proteomics 2020; 21:e1900312. [PMID: 32875713 DOI: 10.1002/pmic.201900312] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/09/2020] [Indexed: 12/24/2022]
Abstract
Multiple types of molecular data for the same set of clinical samples are increasingly available and may be analyzed jointly in an integrative analysis to maximize comprehensive biological insight. This analysis is important as separate analyses of individual omics data types usually do not fully explain disease phenotypes. An increasing number of studies have now been focusing on multi-omics data integration, yet not many studies have included phosphoproteomics data, an important layer for understanding signaling pathways. Multi-omics integration methods with phosphoproteomics data are reviewed in the context of cancer research as well as multi-omics methods papers that would be promising to apply to phosphoproteomics data. Analysis of individual data types is still the major approach even in large cohort proteogenomics studies. Hence, a section is dedicated on possible integrative methods for multi-omics and phosphoproteomics data. In summary, this review provides the readers with both currently used integrative methods previously applied to phosphoproteomics and multi-omics data integration and other algorithms for multi-omics data integration promising for future application to phosphoproteomics data.
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Affiliation(s)
- Giulia Mantini
- Department of Medical Oncology, OncoProteomics Laboratory, CCA 1-60, Amsterdam UMC VUmc-location, De Boelelaan 1117, Amsterdam, 1081 HV, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, OncoProteomics Laboratory, CCA 1-60, Amsterdam UMC VUmc-location, De Boelelaan 1117, Amsterdam, 1081 HV, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, OncoProteomics Laboratory, CCA 1-60, Amsterdam UMC VUmc-location, De Boelelaan 1117, Amsterdam, 1081 HV, The Netherlands
| | - Connie R Jimenez
- Department of Medical Oncology, OncoProteomics Laboratory, CCA 1-60, Amsterdam UMC VUmc-location, De Boelelaan 1117, Amsterdam, 1081 HV, The Netherlands
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Yang W, Chen N, Li L, Chen X, Liu X, Zhang Y, Cui J. Favorable Immune Microenvironment in Patients with EGFR and MAPK Co-Mutations. LUNG CANCER-TARGETS AND THERAPY 2020; 11:59-71. [PMID: 32982525 PMCID: PMC7490071 DOI: 10.2147/lctt.s262822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/13/2020] [Indexed: 12/24/2022]
Abstract
Purpose Although EGFR-mutated patients generally do not benefit from checkpoint inhibitors (ICIs), some patients in the KEYNOTE-001 study consistently benefited from this treatment. This study investigated immune microenvironment characteristics to identify the subgroup of patients that may benefit from ICIs. Materials and Methods Using data from The Cancer Genome Atlas Program (TCGA) and Cancer Proteome Atlas, TMB and protein level of PD-L1 were explored in the patients with EGFR mutations and wild-type patients. Different patterns of EGFR mutations (according to EGFR co-mutation with different downstream pathway genesets) were used to group EGFR mutation population. Estimated infiltration analyses were used to explore changes in the immune microenvironment. Results This study analyzed somatic mutation data from 1287 patients from five cohorts (TCGA, Broad, The Tumour Sequencing Project, Memorial Sloan Kettering Cancer Center, Catalogue Of Somatic Mutations In Cancer database). The probability of EGFR mutation was approximately 14.30% (184/1287) and the co-mutation rate was 11.41% (21/184) in patients with EGFR mutations. Glycosaminoglycan-related pathways were significantly upregulated in the EGFR mutant group. EGFR-mutated patients had lower TMB and PD-L1 protein levels than those in wild-type patients. Increase immature DCs infiltration and decreased NK CD56dim, T gamma delta, cytotoxic, and Th2 cell infiltration were the main immune changes in EGFR-mutated patients. Patients with EGFR-MAPK co-mutations had higher levels of TMB and PD-L1 protein expression. Meanwhile, the co-mutated patients had a similar immune microenvironment as that in wild-type patients. Conclusion In this study, we defined a subgroup of patients with EGFR-MAPK co-mutations. These co-mutated patients may benefit from ICI treatment.
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Affiliation(s)
- Wang Yang
- The Cancer Center of the First Hospital of Jilin University, Changchun, Jilin 130021, People's Republic of China
| | - Naifei Chen
- The Cancer Center of the First Hospital of Jilin University, Changchun, Jilin 130021, People's Republic of China
| | - Lingyu Li
- The Cancer Center of the First Hospital of Jilin University, Changchun, Jilin 130021, People's Republic of China
| | - Xiao Chen
- The Cancer Center of the First Hospital of Jilin University, Changchun, Jilin 130021, People's Republic of China
| | - Xiangliang Liu
- The Cancer Center of the First Hospital of Jilin University, Changchun, Jilin 130021, People's Republic of China
| | - Yongfei Zhang
- The Cancer Center of the First Hospital of Jilin University, Changchun, Jilin 130021, People's Republic of China
| | - Jiuwei Cui
- The Cancer Center of the First Hospital of Jilin University, Changchun, Jilin 130021, People's Republic of China
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Yim SY, Kang SH, Shin JH, Jeong YS, Sohn BH, Um SH, Lee JS. Low ARID1A Expression is Associated with Poor Prognosis in Hepatocellular Carcinoma. Cells 2020; 9:E2002. [PMID: 32878261 PMCID: PMC7564185 DOI: 10.3390/cells9092002] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/26/2020] [Accepted: 07/29/2020] [Indexed: 01/01/2023] Open
Abstract
AT-rich interactive domain 1A (ARID1A) is one of the most frequently mutated genes in hepatocellular carcinoma (HCC), but its clinical significance is not clarified. We aimed to evaluate the clinical significance of low ARID1A expression in HCC. By analyzing the gene expression data of liver from Arid1a-knockout mice, hepatic Arid1a-specific gene expression signature was identified (p < 0.05 and 0.5-fold difference). From this signature, a prediction model was developed to identify tissues lacking Arid1a activity and was applied to gene expression data from three independent cohorts of HCC patients to stratify patients according to ARID1A activity. The molecular features associated with loss of ARID1A were analyzed using The Cancer Genome Atlas (TCGA) multi-platform data, and Ingenuity Pathway Analysis (IPA) was done to uncover potential signaling pathways associated with ARID1A loss. ARID1A inactivation was clinically associated with poor prognosis in all three independent cohorts and was consistently related to poor prognosis subtypes of previously reported gene signatures (highly proliferative, hepatic stem cell, silence of Hippo pathway, and high recurrence signatures). Immune activity, indicated by significantly lower IFNG6 and cytolytic activity scores and enrichment of regulatory T-cell composition, was lower in the ARID1A-low subtype than ARID1A-high subtype. Ingenuity pathway analysis revealed that direct upstream transcription regulators of the ARID1A signature were genes associated with cell cycle, including E2F group, CCND1, and MYC, while tumor suppressors such as TP53, SMAD3, and CTNNB1 were significantly inhibited. ARID1A plays an important role in immune activity and regulating multiple genes involved in HCC development. Low-ARID1A subtype was associated with poor clinical outcome and suggests the possibility of ARID1A as a prognostic biomarker in HCC patients.
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Affiliation(s)
- Sun Young Yim
- Department of Internal Medicine, Korea University College of Medicine, Seoul 136-701, Korea; (S.Y.Y.); (S.H.U.)
| | - Sang Hee Kang
- Department of Surgery, Korea University College of Medicine, Seoul 136-701, Korea;
| | - Ji-Hyun Shin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (J.-H.S.); (Y.S.J.); (B.H.S.)
| | - Yun Seong Jeong
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (J.-H.S.); (Y.S.J.); (B.H.S.)
| | - Bo Hwa Sohn
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (J.-H.S.); (Y.S.J.); (B.H.S.)
| | - Soon Ho Um
- Department of Internal Medicine, Korea University College of Medicine, Seoul 136-701, Korea; (S.Y.Y.); (S.H.U.)
| | - Ju-Seog Lee
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (J.-H.S.); (Y.S.J.); (B.H.S.)
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Xie R, Wen F, Qin Y. The Dysregulation and Prognostic Analysis of STRIPAK Complex Across Cancers. Front Cell Dev Biol 2020; 8:625. [PMID: 32754603 PMCID: PMC7365848 DOI: 10.3389/fcell.2020.00625] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/23/2020] [Indexed: 12/24/2022] Open
Abstract
The striatin-interacting phosphatase and kinase (STRIPAK) is the highly conserved complex, which gains increased attention in physiology and pathology process recently. However, limited studies reported the details of STRIPAK complex in cancers while some results strongly suggested it plays a vital role in tumorigenesis. Hence, we systematically analyzed the molecular and survival profiles of 18 STRIPAK genes to assess the value of STRIPAK complex across cancers. Our findings revealed the low frequencies of DNA aberrances and incomparable expression difference of STRIPAK genes between normal and tumor tissues, but they showed strong prognostic value in cancers, especially the liver hepatocellular carcinoma (LIHC) and kidney renal clear cell carcinoma (KIRC). Interestingly, STRIPAK genes were observed the opposite pattern of survival and expression in the above two cancer types. PPP2R1A and TRAF3IP3 were proposed as the oncogenic genes in LIHC and KIRC, respectively. The STRIPAK genes serve as oncogenes may due to the methylation heterogeneity. Taken together, our comprehensive molecular analysis of STRIPAK complex provides resource to facilitate the understanding of mechanism and utilize the potential therapies to tumors.
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Affiliation(s)
- Ruiling Xie
- Department of Otolaryngology, Head and Neck Surgery, Peking University First Hospital, Beijing, China
| | - Feng Wen
- Department of Otolaryngology, Head and Neck Surgery, Peking University First Hospital, Beijing, China
| | - Yong Qin
- Department of Otolaryngology, Head and Neck Surgery, Peking University First Hospital, Beijing, China
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Prognostic implication of proteomic profiles in head and neck squamous cell carcinoma. Clin Chim Acta 2020; 509:304-309. [PMID: 32569632 DOI: 10.1016/j.cca.2020.06.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/04/2020] [Accepted: 06/12/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND AND OBJECTIVE Head and neck squamous cell carcinoma (HNSCC) is one of the malignant cancers with poor prognosis. However, clinicopathologic and histological criteria were finite to predict the prognosis of HNSCC. We aimed to characterize the proteomic profile of prognosis from HNSCC patients. MATERIAL AND METHODS Reverse phase protein array (RPPA) data in HNSCC were downloaded from The Cancer Proteome Atlas (TCPA). Independent prognostic-related proteins (IPP) were screened by Cox regression model and Kaplan-Meier methods. IPP signature (IPPS) including selected proteins was conducted for prognostic prediction for HNSCC. Protein-protein network analysis and gene ontology (GO) enrichment were used to identify related functional proteins and pathways. RESULTS Based on the IPP, IPPS for HNSCC was constructed: risk score = (1.541* IRF1) + (1.460 * SMAD4) + (1.396 * LKB1) + (0.746* Cyclin E2) + (0.618* Paxillin) + (0.499* p-PEA-15 (Ser116)). The IPPS in HNSCC showed good predictive performance (area under curve = 0.779) with moderate sensitivity and specificity. Protein-protein network analysis and functional enrichment indicated an implication of response to decreased oxygen levels in HNSCC. CONCLUSION The identified proteomic signature might function as a prognostic tool for the management of HNSCC and provide novel target for the treatment of HNSCC.
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Zheng H, Zhang G, Zhang L, Wang Q, Li H, Han Y, Xie L, Yan Z, Li Y, An Y, Dong H, Zhu W, Guo X. Comprehensive Review of Web Servers and Bioinformatics Tools for Cancer Prognosis Analysis. Front Oncol 2020; 10:68. [PMID: 32117725 PMCID: PMC7013087 DOI: 10.3389/fonc.2020.00068] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/15/2020] [Indexed: 01/10/2023] Open
Abstract
Prognostic biomarkers are of great significance to predict the outcome of patients with cancer, to guide the clinical treatments, to elucidate tumorigenesis mechanisms, and offer the opportunity of identifying therapeutic targets. To screen and develop prognostic biomarkers, high throughput profiling methods including gene microarray and next-generation sequencing have been widely applied and shown great success. However, due to the lack of independent validation, only very few prognostic biomarkers have been applied for clinical practice. In order to cross-validate the reliability of potential prognostic biomarkers, some groups have collected the omics datasets (i.e., epigenetics/transcriptome/proteome) with relative follow-up data (such as OS/DSS/PFS) of clinical samples from different cohorts, and developed the easy-to-use online bioinformatics tools and web servers to assist the biomarker screening and validation. These tools and web servers provide great convenience for the development of prognostic biomarkers, for the study of molecular mechanisms of tumorigenesis and progression, and even for the discovery of important therapeutic targets. Aim to help researchers to get a quick learning and understand the function of these tools, the current review delves into the introduction of the usage, characteristics and algorithms of tools, and web servers, such as LOGpc, KM plotter, GEPIA, TCPA, OncoLnc, PrognoScan, MethSurv, SurvExpress, UALCAN, etc., and further help researchers to select more suitable tools for their own research. In addition, all the tools introduced in this review can be reached at http://bioinfo.henu.edu.cn/WebServiceList.html.
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Affiliation(s)
- Hong Zheng
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Guosen Zhang
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Lu Zhang
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Qiang Wang
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Huimin Li
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Yali Han
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Longxiang Xie
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Zhongyi Yan
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Yongqiang Li
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Yang An
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Huan Dong
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Wan Zhu
- Department of Anesthesia, Stanford University, Stanford, CA, United States
| | - Xiangqian Guo
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
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Labrie M, Kendsersky ND, Ma H, Campbell L, Eng J, Chin K, Mills GB. Proteomics advances for precision therapy in ovarian cancer. Expert Rev Proteomics 2019; 16:841-850. [PMID: 31512530 PMCID: PMC6814571 DOI: 10.1080/14789450.2019.1666004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/06/2019] [Indexed: 10/26/2022]
Abstract
Introduction: Due to the relatively low mutation rate and high frequency of copy number variation, finding actionable genetic drivers of high-grade serous carcinoma (HGSC) is a challenging task. Furthermore, emerging studies show that genetic alterations are frequently poorly represented at the protein level adding a layer of complexity. With improvements in large-scale proteomic technologies, proteomics studies have the potential to provide robust analysis of the pathways driving high HGSC behavior. Areas covered: This review summarizes recent large-scale proteomics findings across adequately sized ovarian cancer sample sets. Key words combined with 'ovarian cancer' including 'proteomics', 'proteogenomic', 'reverse-phase protein array', 'mass spectrometry', and 'adaptive response', were used to search PubMed. Expert opinion: Proteomics analysis of HGSC as well as their adaptive responses to therapy can uncover new therapeutic liabilities, which can reduce the emergence of drug resistance and potentially improve patient outcomes. There is a pressing need to better understand how the genomic and epigenomic heterogeneity intrinsic to ovarian cancer is reflected at the protein level and how this information could be used to improve patient outcomes.
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Affiliation(s)
- Marilyne Labrie
- Knight Cancer Institute and Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Nicholas D Kendsersky
- Knight Cancer Institute and Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Hongli Ma
- Knight Cancer Institute and Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Lydia Campbell
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon
| | - Jennifer Eng
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon
| | - Koei Chin
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon
| | - Gordon B Mills
- Knight Cancer Institute and Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, OR, USA
- Department of Systems Biology, University of Texas, MD Anderson Cancer Center, Houston, TX, USA
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Zhang B, Kuster B. Proteomics Is Not an Island: Multi-omics Integration Is the Key to Understanding Biological Systems. Mol Cell Proteomics 2019; 18:S1-S4. [PMID: 31399542 PMCID: PMC6692779 DOI: 10.1074/mcp.e119.001693] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Indexed: 12/18/2022] Open
Affiliation(s)
- Bing Zhang
- ‡Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- §Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Bernhard Kuster
- ¶Chair of Proteomics and Bioanalytics, Technische Universitat Munchen, Freising, Germany
- ‖Bavarian Biomolecular Mass Spectrometry Center, Technische Universitat Munchen, Freising, Germany
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Labrie M, Fang Y, Kendsersky ND, Li J, Liang H, Westin SN, Mitri Z, Mills GB. Using Reverse Phase Protein Array (RPPA) to Identify and Target Adaptive Resistance. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1188:251-266. [PMID: 31820393 PMCID: PMC7382818 DOI: 10.1007/978-981-32-9755-5_14] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Tumor cells and the tumor ecosystem rapidly evolve in response to therapy. This tumor evolution results in the rapid emergence of drug resistance that limits the magnitude and duration of response to therapy including chemotherapy, targeted therapy, and immunotherapy. Thus, there is an urgent need to understand and interdict tumor evolution to improve patient benefit to therapy. Reverse phase protein array (RPPA) provides a powerful tool to evaluate and develop approaches to target the processes underlying one form of tumor evolution: adaptive evolution. Tumor cells and the tumor microenvironment rapidly evolve through rewiring of protein networks to bypass the effects of therapy. In this review, we present the concepts underlying adaptive resistance and use of RPPA in understanding resistance mechanisms and identification of effective drug combinations. We further demonstrate that this novel information is resulting in biomarker-driven trials aimed at targeting adaptive resistance and improving patient outcomes.
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Affiliation(s)
- Marilyne Labrie
- Knight Cancer Institute, Oregon Health and Sciences University, Portland, OR, USA.
| | - Yong Fang
- Knight Cancer Institute, Oregon Health and Sciences University, Portland, OR, USA
| | | | - Jun Li
- Department of Gynecological Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Han Liang
- Department of Gynecological Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Shannon N Westin
- Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Zahi Mitri
- Knight Cancer Institute, Oregon Health and Sciences University, Portland, OR, USA
| | - Gordon B Mills
- Knight Cancer Institute, Oregon Health and Sciences University, Portland, OR, USA
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