1
|
Alagundagi DB, Ghate SD, Shetty P, Gollapalli P, Shetty P, Patil P. Integrated molecular-network analysis reveals infertility-associated key genes and transcription factors in the non-obstructive azoospermia. Eur J Obstet Gynecol Reprod Biol 2023; 288:183-190. [PMID: 37549510 DOI: 10.1016/j.ejogrb.2023.07.023] [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: 11/11/2022] [Revised: 06/05/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND Male infertility is a multifactorial reproductive health problem with complex causes. Non-obstructive azoospermia (NOA) is characterized by failure of spermatogenesis, leading to the absence of spermatozoa in ejaculates. The molecular mechanism underlying the NOA is still not well understood. OBJECTIVES This study aims to identify the key genes involved in male infertility that could be a potential biomarker in the diagnosis and prognosis of azoospermia. STUDY DESIGN The microarray expression profiles dataset GSE45885 and GSE45887 were downloaded from the NCBI's Gene Expression Omnibus (GEO) database and analyzed for male infertility-associated differentially expressed genes (DEGs) using the GEO2R tool. The common DEGs between the two datasets were combined and their protein-protein interaction (PPI) network was constructed using Cytoscape to reveal the hub genes by topology and module analysis. In addition, transcription factors (TFs) and protein kinases regulating the hub genes were identified using the X2K tool. Then, the expression of the hub genes was validated by analyzing the GSE190752 microarray dataset. Further, the PPI network was screened for biological roles and enriched pathways using DAVID software. RESULTS About 256 DEGs associated with NOA were identified and constructed the PPI network to find the infertility-associated proteins. The biological processes linked with these proteins were spermatogenesis, cell differentiation, flagellated sperm motility, and spermatid development. The topology and module analysis of the infertility-associated protein network identified the hub genes TEX38, FAM71F, PRR30, FAM166A, LYZL6, TPPP2, ARMC12, SPACA4, and FAM205A, which were found to be upregulated in the non-obstructive azoospermia. In addition, a total of 23 transcription factors and 3 protein kinases that are regulating these key hub genes were identified. Further these hub genes expression was validated using the microarray data and found that their expression was increased in the testicular biopsies obtained from NOA subjects, compared to healthy individuals. CONCLUSION The identified key genes and its associated transcription factors are known to regulate the infertility-related processes in the non-obstructive azoospermia. Also, the clinical sample-based microarray data validation for the expression of these key hub genes indicates their potentiality to develop them as diagnostic or prognostic biomarkers for NOA.
Collapse
Affiliation(s)
- Dhananjay B Alagundagi
- Central Research Laboratory, K S Hegde Medical Academy, NITTE (Deemed to be University), Mangaluru 575018, Karnataka, India.
| | - Sudeep D Ghate
- Center for Bioinformatics and Biostatistics, NITTE (Deemed to be University), Mangaluru 575018, Karnataka, India.
| | - Prasannakumar Shetty
- Department of Obstetrics and Gynecology, Justice K S Hegde Charitable Hospital, K S Hegde Medical Academy, NITTE (Deemed to be University), Mangaluru 575018, Karnataka, India.
| | - Pavan Gollapalli
- Center for Bioinformatics and Biostatistics, NITTE (Deemed to be University), Mangaluru 575018, Karnataka, India.
| | - Praveenkumar Shetty
- Central Research Laboratory, K S Hegde Medical Academy, NITTE (Deemed to be University), Mangaluru 575018, Karnataka, India; Department of Biochemistry, K S Hegde Medical Academy, NITTE (Deemed to be University), Mangaluru 575018, Karnataka, India.
| | - Prakash Patil
- Central Research Laboratory, K S Hegde Medical Academy, NITTE (Deemed to be University), Mangaluru 575018, Karnataka, India.
| |
Collapse
|
2
|
Zhai LH, Chen KF, Hao BB, Tan MJ. Proteomic characterization of post-translational modifications in drug discovery. Acta Pharmacol Sin 2022; 43:3112-3129. [PMID: 36372853 PMCID: PMC9712763 DOI: 10.1038/s41401-022-01017-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/07/2022] [Indexed: 11/15/2022] Open
Abstract
Protein post-translational modifications (PTMs), which are usually enzymatically catalyzed, are major regulators of protein activity and involved in almost all celluar processes. Dysregulation of PTMs is associated with various types of diseases. Therefore, PTM regulatory enzymes represent as an attractive and important class of targets in drug research and development. Inhibitors against kinases, methyltransferases, deacetyltransferases, ubiquitin ligases have achieved remarkable success in clinical application. Mass spectrometry-based proteomics technologies serve as a powerful approach for system-wide characterization of PTMs, which facilitates the identification of drug targets, elucidation of the mechanisms of action of drugs, and discovery of biomakers in personalized therapy. In this review, we summarize recent advances of proteomics-based studies on PTM targeting drugs and discuss how proteomics strategies facilicate drug target identification, mechanism elucidation, and new therapy development in precision medicine.
Collapse
Affiliation(s)
- Lin-Hui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Zhongshan Institute of Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Science, Zhongshan, 528400, China
| | - Kai-Feng Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bing-Bing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Min-Jia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Zhongshan Institute of Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Science, Zhongshan, 528400, China.
| |
Collapse
|
3
|
Noor F, Tahir ul Qamar M, Ashfaq UA, Albutti A, Alwashmi ASS, Aljasir MA. Network Pharmacology Approach for Medicinal Plants: Review and Assessment. Pharmaceuticals (Basel) 2022; 15:572. [PMID: 35631398 PMCID: PMC9143318 DOI: 10.3390/ph15050572] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 12/13/2022] Open
Abstract
Natural products have played a critical role in medicine due to their ability to bind and modulate cellular targets involved in disease. Medicinal plants hold a variety of bioactive scaffolds for the treatment of multiple disorders. The less adverse effects, affordability, and easy accessibility highlight their potential in traditional remedies. Identifying pharmacological targets from active ingredients of medicinal plants has become a hot topic for biomedical research to generate innovative therapies. By developing an unprecedented opportunity for the systematic investigation of traditional medicines, network pharmacology is evolving as a systematic paradigm and becoming a frontier research field of drug discovery and development. The advancement of network pharmacology has opened up new avenues for understanding the complex bioactive components found in various medicinal plants. This study is attributed to a comprehensive summary of network pharmacology based on current research, highlighting various active ingredients, related techniques/tools/databases, and drug discovery and development applications. Moreover, this study would serve as a protocol for discovering novel compounds to explore the full range of biological potential of traditionally used plants. We have attempted to cover this vast topic in the review form. We hope it will serve as a significant pioneer for researchers working with medicinal plants by employing network pharmacology approaches.
Collapse
Affiliation(s)
- Fatima Noor
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (F.N.); (M.T.u.Q.)
| | - Muhammad Tahir ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (F.N.); (M.T.u.Q.)
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan; (F.N.); (M.T.u.Q.)
| | - Aqel Albutti
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Ameen S. S. Alwashmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (A.S.S.A.); (M.A.A.)
| | - Mohammad Abdullah Aljasir
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (A.S.S.A.); (M.A.A.)
| |
Collapse
|
4
|
Andrades R, Recamonde-Mendoza M. Machine learning methods for prediction of cancer driver genes: a survey paper. Brief Bioinform 2022; 23:6551145. [PMID: 35323900 DOI: 10.1093/bib/bbac062] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/06/2022] [Accepted: 02/08/2022] [Indexed: 12/21/2022] Open
Abstract
Identifying the genes and mutations that drive the emergence of tumors is a critical step to improving our understanding of cancer and identifying new directions for disease diagnosis and treatment. Despite the large volume of genomics data, the precise detection of driver mutations and their carrying genes, known as cancer driver genes, from the millions of possible somatic mutations remains a challenge. Computational methods play an increasingly important role in discovering genomic patterns associated with cancer drivers and developing predictive models to identify these elements. Machine learning (ML), including deep learning, has been the engine behind many of these efforts and provides excellent opportunities for tackling remaining gaps in the field. Thus, this survey aims to perform a comprehensive analysis of ML-based computational approaches to identify cancer driver mutations and genes, providing an integrated, panoramic view of the broad data and algorithmic landscape within this scientific problem. We discuss how the interactions among data types and ML algorithms have been explored in previous solutions and outline current analytical limitations that deserve further attention from the scientific community. We hope that by helping readers become more familiar with significant developments in the field brought by ML, we may inspire new researchers to address open problems and advance our knowledge towards cancer driver discovery.
Collapse
Affiliation(s)
- Renan Andrades
- Institute of Informatics, Universidade Federal do Rio Grande do Sul, Porto Alegre/RS, Brazil.,Bioinformatics Core, Hospital de Clínicas de Porto Alegre, Porto Alegre/RS, Brazil
| | - Mariana Recamonde-Mendoza
- Institute of Informatics, Universidade Federal do Rio Grande do Sul, Porto Alegre/RS, Brazil.,Bioinformatics Core, Hospital de Clínicas de Porto Alegre, Porto Alegre/RS, Brazil
| |
Collapse
|
5
|
Simpson CM, Gnad F. Applying graph database technology for analyzing perturbed co-expression networks in cancer. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:6029398. [PMID: 33306799 PMCID: PMC7731929 DOI: 10.1093/database/baaa110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 09/20/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022]
Abstract
Graph representations provide an elegant solution to capture and analyze complex molecular mechanisms in the cell. Co-expression networks are undirected graph representations of transcriptional co-behavior indicating (co-)regulations, functional modules or even physical interactions between the corresponding gene products. The growing avalanche of available RNA sequencing (RNAseq) data fuels the construction of such networks, which are usually stored in relational databases like most other biological data. Inferring linkage by recursive multiple-join statements, however, is computationally expensive and complex to design in relational databases. In contrast, graph databases store and represent complex interconnected data as nodes, edges and properties, making it fast and intuitive to query and analyze relationships. While graph-based database technologies are on their way from a fringe domain to going mainstream, there are only a few studies reporting their application to biological data. We used the graph database management system Neo4j to store and analyze co-expression networks derived from RNAseq data from The Cancer Genome Atlas. Comparing co-expression in tumors versus healthy tissues in six cancer types revealed significant perturbation tracing back to erroneous or rewired gene regulation. Applying centrality, community detection and pathfinding graph algorithms uncovered the destruction or creation of central nodes, modules and relationships in co-expression networks of tumors. Given the speed, accuracy and straightforwardness of managing these densely connected networks, we conclude that graph databases are ready for entering the arena of biological data.
Collapse
Affiliation(s)
- Claire M Simpson
- Department of Bioinformatics and Data Science, Cell Signaling Technology Inc., 3 Trask Lane, Danvers, MA 01923, USA
| | - Florian Gnad
- Department of Bioinformatics and Data Science, Cell Signaling Technology Inc., 3 Trask Lane, Danvers, MA 01923, USA
| |
Collapse
|
6
|
Lyu J, Li JJ, Su J, Peng F, Chen YE, Ge X, Li W. DORGE: Discovery of Oncogenes and tumoR suppressor genes using Genetic and Epigenetic features. SCIENCE ADVANCES 2020; 6:6/46/eaba6784. [PMID: 33177077 PMCID: PMC7673741 DOI: 10.1126/sciadv.aba6784] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 09/29/2020] [Indexed: 05/09/2023]
Abstract
Data-driven discovery of cancer driver genes, including tumor suppressor genes (TSGs) and oncogenes (OGs), is imperative for cancer prevention, diagnosis, and treatment. Although epigenetic alterations are important for tumor initiation and progression, most known driver genes were identified based on genetic alterations alone. Here, we developed an algorithm, DORGE (Discovery of Oncogenes and tumor suppressoR genes using Genetic and Epigenetic features), to identify TSGs and OGs by integrating comprehensive genetic and epigenetic data. DORGE identified histone modifications as strong predictors for TSGs, and it found missense mutations, super enhancers, and methylation differences as strong predictors for OGs. We extensively validated DORGE-predicted cancer driver genes using independent functional genomics data. We also found that DORGE-predicted dual-functional genes (both TSGs and OGs) are enriched at hubs in protein-protein interaction and drug-gene networks. Overall, our study has deepened the understanding of epigenetic mechanisms in tumorigenesis and revealed previously undetected cancer driver genes.
Collapse
Affiliation(s)
- Jie Lyu
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Jianzhong Su
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fanglue Peng
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yiling Elaine Chen
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xinzhou Ge
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA.
| |
Collapse
|
7
|
Yamada Y, Miyamoto T, Higuchi S, Ono M, Kobara H, Asaka R, Ando H, Suzuki A, Shiozawa T. cDNA expression library screening revealed novel functional genes involved in clear cell carcinogenesis of the ovary in vitro. J OBSTET GYNAECOL 2020; 41:100-105. [PMID: 32157937 DOI: 10.1080/01443615.2020.1716310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In order to identify genes involved in the pathogenesis of clear cell carcinoma of the ovary (CCC), functional screening using a cDNA expression library was performed. We extracted mRNA from a CCC cell line (RMG-1), established a cDNA library using a retroviral vector, transfected that library into mouse NIH3T3 cells and sequenced the resultant foci. The tissue-type specific expression of isolated genes and their transforming activities were evaluated. Seven genes were isolated. Of these genes, the mRNA expression of SEC61B and DVL1 is significantly stronger in CCC than in other histological types (p < .05). Immunohistochemical staining reveals the stronger expression of SEC61B and C1ORF38 than normal ovarian tissues (p < .05). Focus formation is confirmed by the transfection of SEC61B, C1ORF38, and DVL1 into NIH3T3 cells. The present study identified novel genes including SEC61B, C1ORF38, and DVL1, involved in the pathogenesis of CCC. These genes may be additional therapeutic targets for CCC.Impact statementWhat is already known on this subject? Several important genetic abnormalities, including ARID1A and PIK3CA mutations, have been reported in ovarian clear cell carcinoma (CCC).What the results of this study add? SEC61B, C1ORF38, and DVL1 were newly detected as candidate genes involved in ovarian clear cell carcinogenesis.What the implications are of these findings for clinical practice and/or further research? Functional screening using a cDNA expression library may be a useful technique to identify functional genes for pathogenesis. The information obtained using this technique may provide new therapeutic targets of CCC.
Collapse
Affiliation(s)
- Yasushi Yamada
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Japan
| | - Tsutomu Miyamoto
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Japan
| | - Shotaro Higuchi
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Japan
| | - Motoki Ono
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Japan
| | - Hisanori Kobara
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Japan
| | - Ryoichi Asaka
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Japan
| | - Hirofumi Ando
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Japan
| | - Akihisa Suzuki
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Japan
| | - Tanri Shiozawa
- Department of Obstetrics and Gynecology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Japan
| |
Collapse
|
8
|
Simpson CM, Zhang B, Hornbeck PV, Gnad F. Systematic analysis of the intersection of disease mutations with protein modifications. BMC Med Genomics 2019; 12:109. [PMID: 31345222 PMCID: PMC6657027 DOI: 10.1186/s12920-019-0543-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Perturbed posttranslational modification (PTM) landscapes commonly cause pathological phenotypes. The Cancer Genome Atlas (TCGA) project profiles thousands of tumors allowing the identification of spontaneous cancer-driving mutations, while Uniprot and dbSNP manage genetic disease-associated variants in the human population. PhosphoSitePlus (PSP) is the most comprehensive resource for studying experimentally observed PTM sites and the only repository with daily updates on functional annotations for many of these sites. To elucidate altered PTM landscapes on a large scale, we integrated disease-associated mutations from TCGA, Uniprot, and dbSNP with PTM sites from PhosphoSitePlus. We characterized each dataset individually, compared somatic with germline mutations, and analyzed PTM sites intersecting directly with disease variants. To assess the impact of mutations in the flanking regions of phosphosites, we developed DeltaScansite, a pipeline that compares Scansite predictions on wild type versus mutated sequences. Disease mutations are also visualized in PhosphoSitePlus. RESULTS Characterization of somatic variants revealed oncoprotein-like mutation profiles of U2AF1, PGM5, and several other proteins, showing alteration patterns similar to germline mutations. The union of all datasets uncovered previously unknown losses and gains of PTM events in diseases unevenly distributed across different PTM types. Focusing on phosphorylation, our DeltaScansite workflow predicted perturbed signaling networks consistent with calculations by the machine learning method MIMP. CONCLUSIONS We discovered oncoprotein-like profiles in TCGA and mutations that presumably modify protein function by impacting PTM sites directly or by rewiring upstream regulation. The resulting datasets are enriched with functional annotations from PhosphoSitePlus and present a unique resource for potential biomarkers or disease drivers.
Collapse
Affiliation(s)
- Claire M Simpson
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc, Danvers, MA, USA
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bin Zhang
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc, Danvers, MA, USA
| | - Peter V Hornbeck
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc, Danvers, MA, USA
| | - Florian Gnad
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc, Danvers, MA, USA.
| |
Collapse
|
9
|
Baldi GG, Orbach D, Bertulli R, Magni C, Sironi G, Casanova M, Ferrari A. Standard treatment and emerging drugs for managing synovial sarcoma: adult's and pediatric oncologist perspective. Expert Opin Emerg Drugs 2019; 24:43-53. [PMID: 30841761 DOI: 10.1080/14728214.2019.1591367] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION in this review we discuss the standard of care for both pediatric and adult synovial sarcoma (SS), the prognostic differences between them, and the treatments available for localized and advanced diseases. We also overview the biology and the recent drugs under consideration in clinical trials on SS. Areas covered: we focus on new targeted therapies being investigated for advanced SS, especially anti-angiogenic drugs, and immunotherapy. We review all the published data and ongoing trials dedicated to SS or to soft tissue sarcoma in general, paying particular attention to the results obtained in SS patients. Expert opinion: we expect new treatment strategies to become available for SS in the near future. The ongoing and published trials on targeted therapies and immunotherapy mainly concern adult patients, but the somatic biology of pediatric SS has some similarities as in adult disease. A stronger cooperation between adult and pediatric oncologists in recent years has led to a more shared effort to find new treatment strategies for advanced SS patients, regardless of their age.
Collapse
Affiliation(s)
- Giacomo G Baldi
- a "Sandro Pitigliani" Medical Oncology Department , Hospital of Prato , Prato , Italy
| | - Daniel Orbach
- b SIREDO Oncology Center , PSL University, Institut Curie , Paris , France
| | - Rossella Bertulli
- c Medical Oncology Unit 2, Medical Oncology Department , Fondazione IRCCS Istituto Nazionale dei Tumori , Milan , Italy
| | - Chiara Magni
- d Pediatric Oncology Unit , Fondazione IRCCS Istituto Nazionale dei Tumori , Milan , Italy
| | - Giovanna Sironi
- d Pediatric Oncology Unit , Fondazione IRCCS Istituto Nazionale dei Tumori , Milan , Italy
| | - Michela Casanova
- d Pediatric Oncology Unit , Fondazione IRCCS Istituto Nazionale dei Tumori , Milan , Italy
| | - Andrea Ferrari
- d Pediatric Oncology Unit , Fondazione IRCCS Istituto Nazionale dei Tumori , Milan , Italy
| |
Collapse
|
10
|
Wojcik JB, Marchione DM, Sidoli S, Djedid A, Lisby A, Majewski J, Garcia BA. Epigenomic Reordering Induced by Polycomb Loss Drives Oncogenesis but Leads to Therapeutic Vulnerabilities in Malignant Peripheral Nerve Sheath Tumors. Cancer Res 2019; 79:3205-3219. [PMID: 30898839 DOI: 10.1158/0008-5472.can-18-3704] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/17/2019] [Accepted: 03/18/2019] [Indexed: 12/28/2022]
Abstract
Malignant peripheral nerve sheath tumor (MPNST) is an aggressive sarcoma with recurrent loss-of-function alterations in polycomb-repressive complex 2 (PRC2), a histone-modifying complex involved in transcriptional silencing. To understand the role of PRC2 loss in pathogenesis and identify therapeutic targets, we conducted parallel global epigenomic and proteomic analysis of archival formalin-fixed, paraffin-embedded (FFPE) human MPNST with and without PRC2 loss (MPNSTLOSS vs. MPNSTRET). Loss of PRC2 resulted in increased histone posttranslational modifications (PTM) associated with active transcription, most notably H3K27Ac and H3K36me2, whereas repressive H3K27 di- and trimethylation (H3K27me2/3) marks were globally lost without a compensatory gain in other repressive PTMs. Instead, DNA methylation globally increased in MPNSTLOSS. Epigenomic changes were associated with upregulation of proteins in growth pathways and reduction in IFN signaling and antigen presentation, suggesting a role for epigenomic changes in tumor progression and immune evasion, respectively. These changes also resulted in therapeutic vulnerabilities. Knockdown of NSD2, the methyltransferase responsible for H3K36me2, restored MHC expression and induced interferon pathway expression in a manner similar to PRC2 restoration. MPNSTLOSS were also highly sensitive to DNA methyltransferase and histone deacetylase (HDAC) inhibitors. Overall, these data suggest that global loss of PRC2-mediated repression renders MPNST differentially dependent on DNA methylation to maintain transcriptional integrity and makes them susceptible to therapeutics that promote aberrant transcription initiation. SIGNIFICANCE: Global profiling of histone PTMs and protein expression in archival human MPNST illustrates how PRC2 loss promotes oncogenesis but renders tumors vulnerable to pharmacologic modulation of transcription.See related commentary by Natarajan and Venneti, p. 3172.
Collapse
Affiliation(s)
- John B Wojcik
- Department of Biochemistry and Biophysics, and Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania. .,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Dylan M Marchione
- Department of Biochemistry and Biophysics, and Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Simone Sidoli
- Department of Biochemistry and Biophysics, and Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anissa Djedid
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Amanda Lisby
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jacek Majewski
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, and Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| |
Collapse
|
11
|
Doll S, Gnad F, Mann M. The Case for Proteomics and Phospho-Proteomics in Personalized Cancer Medicine. Proteomics Clin Appl 2019; 13:e1800113. [PMID: 30790462 PMCID: PMC6519247 DOI: 10.1002/prca.201800113] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/01/2019] [Indexed: 02/06/2023]
Abstract
The concept of personalized medicine is predominantly been pursued through genomic and transcriptomic technologies, leading to the identification of multiple mutations in a large variety of cancers. However, it has proven challenging to distinguish driver and passenger mutations and to deal with tumor heterogeneity and resistant clonal populations. More generally, these heterogeneous mutation patterns do not in themselves predict the tumor phenotype. Analysis of the expressed proteins in a tumor and their modification states reveals if and how these mutations are translated to the functional level. It is already known that proteomic changes including posttranslational modifications are crucial drivers of oncogenesis, but proteomics technology has only recently become comparable in depth and accuracy to RNAseq. These advances also allow the rapid and highly sensitive analysis of formalin-fixed and paraffin-embedded biobank tissues, on both the proteome and phosphoproteome levels. In this perspective, pioneering mass spectrometry-based proteomic studies are highlighted that pave the way toward clinical implementation. It is argued that proteomics and phosphoproteomics could provide the missing link to make omics analysis actionable in the clinic.
Collapse
Affiliation(s)
- Sophia Doll
- Department of Proteomics and Signal TransductionMax Planck Institute of Biochemistry82152MartinsriedGermany
- NNF Center for Protein ResearchFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Florian Gnad
- Department of Bioinformatics and Computational BiologyCell Signaling Technology Inc01923DanversMAUSA
| | - Matthias Mann
- Department of Proteomics and Signal TransductionMax Planck Institute of Biochemistry82152MartinsriedGermany
- NNF Center for Protein ResearchFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| |
Collapse
|
12
|
Genomic characterization of genes encoding histone acetylation modulator proteins identifies therapeutic targets for cancer treatment. Nat Commun 2019; 10:733. [PMID: 30760718 PMCID: PMC6374416 DOI: 10.1038/s41467-019-08554-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/18/2019] [Indexed: 02/07/2023] Open
Abstract
A growing emphasis in anticancer drug discovery efforts has been on targeting histone acetylation modulators. Here we comprehensively analyze the genomic alterations of the genes encoding histone acetylation modulator proteins (HAMPs) in the Cancer Genome Atlas cohort and observe that HAMPs have a high frequency of focal copy number alterations and recurrent mutations, whereas transcript fusions of HAMPs are relatively rare genomic events in common adult cancers. Collectively, 86.3% (63/73) of HAMPs have recurrent alterations in at least 1 cancer type and 16 HAMPs, including 9 understudied HAMPs, are identified as putative therapeutic targets across multiple cancer types. For example, the recurrent focal amplification of BRD9 is observed in 9 cancer types and genetic depletion of BRD9 inhibits tumor growth. Our systematic genomic analysis of HAMPs across a large-scale cancer specimen cohort may facilitate the identification and prioritization of potential drug targets and selection of suitable patients for precision treatment. Targeting histone acetylation modulators (HAMPs) is a promising avenue of drug discovery in cancer research. Here, the authors integrate multi-dimensional genomic profiles to systematically investigate recurrent genomic alterations in HAMPs, identifying potential therapeutic targets for precision epigenetic treatment.
Collapse
|
13
|
Hornbeck PV, Kornhauser JM, Latham V, Murray B, Nandhikonda V, Nord A, Skrzypek E, Wheeler T, Zhang B, Gnad F. 15 years of PhosphoSitePlus®: integrating post-translationally modified sites, disease variants and isoforms. Nucleic Acids Res 2019; 47:D433-D441. [PMID: 30445427 PMCID: PMC6324072 DOI: 10.1093/nar/gky1159] [Citation(s) in RCA: 182] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 10/26/2018] [Accepted: 11/09/2018] [Indexed: 12/18/2022] Open
Abstract
For 15 years the mission of PhosphoSitePlus® (PSP, https://www.phosphosite.org) has been to provide comprehensive information and tools for the study of mammalian post-translational modifications (PTMs). The number of unique PTMs in PSP is now more than 450 000 from over 22 000 articles and thousands of MS datasets. The most important areas of growth in PSP are in disease and isoform informatics. Germline mutations associated with inherited diseases and somatic cancer mutations have been added to the database and can now be viewed along with PTMs and associated quantitative information on novel 'lollipop' plots. These plots enable researchers to interactively visualize the overlap between disease variants and PTMs, and to identify mutations that may alter phenotypes by rewiring signaling networks. We are expanding the sequence space to include over 30 000 human and mouse isoforms to enable researchers to explore the important but understudied biology of isoforms. This represents a necessary expansion of sequence space to accommodate the growing precision and depth of coverage enabled by ongoing advances in mass spectrometry. Isoforms are aligned using a new algorithm. Exploring the worlds of PTMs and disease mutations in the entire isoform space will hopefully lead to new biomarkers, therapeutic targets, and insights into isoform biology.
Collapse
Affiliation(s)
- Peter V Hornbeck
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| | - Jon M Kornhauser
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| | - Vaughan Latham
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| | - Beth Murray
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| | - Vidhisha Nandhikonda
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| | - Alex Nord
- University of Montana, Missoula, MT, USA
| | - Elżbieta Skrzypek
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| | | | - Bin Zhang
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| | - Florian Gnad
- Department of Bioinformatics and Computational Biology, Cell Signaling Technology Inc., Danvers, MA, USA
| |
Collapse
|
14
|
Schulten HJ, Bangash M, Karim S, Dallol A, Hussein D, Merdad A, Al-Thoubaity FK, Al-Maghrabi J, Jamal A, Al-Ghamdi F, Choudhry H, Baeesa SS, Chaudhary AG, Al-Qahtani MH. Comprehensive molecular biomarker identification in breast cancer brain metastases. J Transl Med 2017; 15:269. [PMID: 29287594 PMCID: PMC5747948 DOI: 10.1186/s12967-017-1370-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/18/2017] [Indexed: 01/09/2023] Open
Abstract
Background Breast cancer brain metastases (BCBM) develop in about 20–30% of breast cancer (BC) patients. BCBM are associated with dismal prognosis not at least due to lack of valuable molecular therapeutic targets. The aim of the study was to identify new molecular biomarkers and targets in BCBM by using complementary state-of-the-art techniques. Methods We compared array expression profiles of three BCBM with 16 non-brain metastatic BC and 16 primary brain tumors (prBT) using a false discovery rate (FDR) p < 0.05 and fold change (FC) > 2. Biofunctional analysis was conducted on the differentially expressed probe sets. High-density arrays were employed to detect copy number variations (CNVs) and whole exome sequencing (WES) with paired-end reads of 150 bp was utilized to detect gene mutations in the three BCBM. Results The top 370 probe sets that were differentially expressed between BCBM and both BC and prBT were in the majority comparably overexpressed in BCBM and included, e.g. the coding genes BCL3, BNIP3, BNIP3P1, BRIP1, CASP14, CDC25A, DMBT1, IDH2, E2F1, MYCN, RAD51, RAD54L, and VDR. A number of small nucleolar RNAs (snoRNAs) were comparably overexpressed in BCBM and included SNORA1, SNORA2A, SNORA9, SNORA10, SNORA22, SNORA24, SNORA30, SNORA37, SNORA38, SNORA52, SNORA71A, SNORA71B, SNORA71C, SNORD13P2, SNORD15A, SNORD34, SNORD35A, SNORD41, SNORD53, and SCARNA22. The top canonical pathway was entitled, role of BRCA1 in DNA damage response. Network analysis revealed key nodes as Akt, ERK1/2, NFkB, and Ras in a predicted activation stage. Downregulated genes in a data set that was shared between BCBM and prBT comprised, e.g. BC cell line invasion markers JUN, MMP3, TFF1, and HAS2. Important cancer genes affected by CNVs included TP53, BRCA1, BRCA2, ERBB2, IDH1, and IDH2. WES detected numerous mutations, some of which affecting BC associated genes as CDH1, HEPACAM, and LOXHD1. Conclusions Using complementary molecular genetic techniques, this study identified shared and unshared molecular events in three highly aberrant BCBM emphasizing the challenge to detect new molecular biomarkers and targets with translational implications. Among new findings with the capacity to gain clinical relevance is the detection of overexpressed snoRNAs known to regulate some critical cellular functions as ribosome biogenesis. Electronic supplementary material The online version of this article (10.1186/s12967-017-1370-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hans-Juergen Schulten
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Mohammed Bangash
- Division of Neurosurgery, Department of Surgery, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Sajjad Karim
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ashraf Dallol
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Deema Hussein
- King Fahad Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Adnan Merdad
- Department of Surgery, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Fatma K Al-Thoubaity
- Department of Surgery, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Jaudah Al-Maghrabi
- Department of Pathology, Faculty of Medicine, King Abdulaziz University Hospital, Jeddah, Saudi Arabia.,Department of Pathology, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Awatif Jamal
- Department of Pathology, Faculty of Medicine, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Fahad Al-Ghamdi
- Department of Pathology, Faculty of Medicine, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Hani Choudhry
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Saleh S Baeesa
- Division of Neurosurgery, Department of Surgery, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Adeel G Chaudhary
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed H Al-Qahtani
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
15
|
Abstract
Human malignancies are driven by heritable alterations that lead to unchecked cellular proliferation, invasive growth and distant spread. Heritable changes can arise from changes in DNA sequence, or, alternatively, through altered gene expression rooted in epigenetic mechanisms. In recent years, high-throughput sequencing of tumor genomes has revealed a central role for mutations in epigenetic regulatory complexes in oncogenic processes. Through interactions with or direct modifications of chromatin, these proteins help control the accessibility of genes, and thus the transcriptional profile of a cell. Dysfunction in these proteins can lead to activation of oncogenic pathways or silencing of tumor suppressors. Although epigenetic regulators are altered across a broad spectrum of human malignancies, they play a particularly central role in tumors of mesenchymal and neuroectodermal origin. This review will focus on recent advances in the understanding of the molecular pathogenesis of a subset of tumors in which alterations in the polycomb family of chromatin modifying complexes, the SWI/SNF family of nucleosome remodelers, and histones play a central role in disease pathogenesis. Although this review will focus predominantly on the molecular mechanisms underlying these tumors, each section will also highlight areas in which an understanding of the molecular pathogenesis of these diseases has led to the adoption of novel immunohistochemical and molecular markers.
Collapse
|
16
|
Toth R, Scherer D, Kelemen LE, Risch A, Hazra A, Balavarca Y, Issa JPJ, Moreno V, Eeles RA, Ogino S, Wu X, Ye Y, Hung RJ, Goode EL, Ulrich CM. Genetic Variants in Epigenetic Pathways and Risks of Multiple Cancers in the GAME-ON Consortium. Cancer Epidemiol Biomarkers Prev 2017; 26:816-825. [PMID: 28115406 PMCID: PMC6054308 DOI: 10.1158/1055-9965.epi-16-0728] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 11/16/2022] Open
Abstract
Background: Epigenetic disturbances are crucial in cancer initiation, potentially with pleiotropic effects, and may be influenced by the genetic background.Methods: In a subsets (ASSET) meta-analytic approach, we investigated associations of genetic variants related to epigenetic mechanisms with risks of breast, lung, colorectal, ovarian and prostate carcinomas using 51,724 cases and 52,001 controls. False discovery rate-corrected P values (q values < 0.05) were considered statistically significant.Results: Among 162,887 imputed or genotyped variants in 555 candidate genes, SNPs in eight genes were associated with risk of more than one cancer type. For example, variants in BABAM1 were confirmed as a susceptibility locus for squamous cell lung, overall breast, estrogen receptor (ER)-negative breast, and overall prostate, and overall serous ovarian cancer; the most significant variant was rs4808076 [OR = 1.14; 95% confidence interval (CI) = 1.10-1.19; q = 6.87 × 10-5]. DPF1 rs12611084 was inversely associated with ER-negative breast, endometrioid ovarian, and overall and aggressive prostate cancer risk (OR = 0.93; 95% CI = 0.91-0.96; q = 0.005). Variants in L3MBTL3 were associated with colorectal, overall breast, ER-negative breast, clear cell ovarian, and overall and aggressive prostate cancer risk (e.g., rs9388766: OR = 1.06; 95% CI = 1.03-1.08; q = 0.02). Variants in TET2 were significantly associated with overall breast, overall prostate, overall ovarian, and endometrioid ovarian cancer risk, with rs62331150 showing bidirectional effects. Analyses of subpathways did not reveal gene subsets that contributed disproportionately to susceptibility.Conclusions: Functional and correlative studies are now needed to elucidate the potential links between germline genotype, epigenetic function, and cancer etiology.Impact: This approach provides novel insight into possible pleiotropic effects of genes involved in epigenetic processes. Cancer Epidemiol Biomarkers Prev; 26(6); 816-25. ©2017 AACR.
Collapse
Affiliation(s)
- Reka Toth
- National Center for Tumor Diseases and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominique Scherer
- National Center for Tumor Diseases and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Linda E Kelemen
- Medical University of South Carolina and Hollings Cancer Center, Charleston, South Carolina
| | - Angela Risch
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Cancer Research and Epigenetics, Department of Molecular Biology, University of Salzburg, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Aditi Hazra
- Brigham and Women's Hospital, Harvard Medical School, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yesilda Balavarca
- National Center for Tumor Diseases and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Victor Moreno
- Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | | | - Shuji Ogino
- Department of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- University of Toronto, Toronto, Canada
| | - Ellen L Goode
- Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Cornelia M Ulrich
- National Center for Tumor Diseases and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Fred Hutchinson Cancer Research Center, Seattle, Washington
- Huntsman Cancer Institute, Salt Lake City, Utah
| |
Collapse
|
17
|
Nam S. Databases and tools for constructing signal transduction networks in cancer. BMB Rep 2017; 50:12-19. [PMID: 27502015 PMCID: PMC5319659 DOI: 10.5483/bmbrep.2017.50.1.135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Indexed: 12/22/2022] Open
Abstract
Traditionally, biologists have devoted their careers to studying individual biological entities of their own interest, partly due to lack of available data regarding that entity. Large, high-throughput data, too complex for conventional processing methods (i.e., “big data”), has accumulated in cancer biology, which is freely available in public data repositories. Such challenges urge biologists to inspect their biological entities of interest using novel approaches, firstly including repository data retrieval. Essentially, these revolutionary changes demand new interpretations of huge datasets at a systems-level, by so called “systems biology”. One of the representative applications of systems biology is to generate a biological network from high-throughput big data, providing a global map of molecular events associated with specific phenotype changes. In this review, we introduce the repositories of cancer big data and cutting-edge systems biology tools for network generation, and improved identification of therapeutic targets.
Collapse
Affiliation(s)
- Seungyoon Nam
- Department of Life Sciences, Gachon University, Seongnam 13120; Department of Genome Medicine and Science, College of Medicine, Gachon University; Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Incheon 21565, Korea
| |
Collapse
|
18
|
Rodger EJ, Chatterjee A. The epigenomic basis of common diseases. Clin Epigenetics 2017; 9:5. [PMID: 28149333 PMCID: PMC5270348 DOI: 10.1186/s13148-017-0313-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/13/2017] [Indexed: 12/24/2022] Open
Abstract
A report of the 6th Epigenomics of Common Diseases Conference held at the Wellcome Genome Campus in Hinxton, Cambridge, UK, on 1-4 November 2016.
Collapse
Affiliation(s)
- Euan J. Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, Hanover Street, P.O. Box 56, Dunedin, 9054 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Hanover Street, P.O. Box 56, Dunedin, 9054 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand
| |
Collapse
|
19
|
A cloud-based workflow to quantify transcript-expression levels in public cancer compendia. Sci Rep 2016; 6:39259. [PMID: 27982081 PMCID: PMC5159871 DOI: 10.1038/srep39259] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/22/2016] [Indexed: 01/08/2023] Open
Abstract
Public compendia of sequencing data are now measured in petabytes. Accordingly, it is infeasible for researchers to transfer these data to local computers. Recently, the National Cancer Institute began exploring opportunities to work with molecular data in cloud-computing environments. With this approach, it becomes possible for scientists to take their tools to the data and thereby avoid large data transfers. It also becomes feasible to scale computing resources to the needs of a given analysis. We quantified transcript-expression levels for 12,307 RNA-Sequencing samples from the Cancer Cell Line Encyclopedia and The Cancer Genome Atlas. We used two cloud-based configurations and examined the performance and cost profiles of each configuration. Using preemptible virtual machines, we processed the samples for as little as $0.09 (USD) per sample. As the samples were processed, we collected performance metrics, which helped us track the duration of each processing step and quantified computational resources used at different stages of sample processing. Although the computational demands of reference alignment and expression quantification have decreased considerably, there remains a critical need for researchers to optimize preprocessing steps. We have stored the software, scripts, and processed data in a publicly accessible repository (https://osf.io/gqrz9).
Collapse
|
20
|
Gnad F, Wallin J, Edgar K, Doll S, Arnott D, Robillard L, Kirkpatrick DS, Stokes MP, Vijapurkar U, Hatzivassiliou G, Friedman LS, Belvin M. Quantitative phosphoproteomic analysis of the PI3K-regulated signaling network. Proteomics 2016; 16:1992-7. [DOI: 10.1002/pmic.201600118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/08/2016] [Accepted: 06/07/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Florian Gnad
- Department of Bioinformatics and Computational Biology; Genentech Inc; South San Francisco CA USA
| | - Jeffrey Wallin
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | - Kyle Edgar
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | - Sophia Doll
- Department of Protein Chemistry; Genentech Inc; South San Francisco CA USA
| | - David Arnott
- Department of Protein Chemistry; Genentech Inc; South San Francisco CA USA
| | - Liliane Robillard
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | | | | | - Ulka Vijapurkar
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | | | - Lori S. Friedman
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| | - Marcia Belvin
- Department of Translational Oncology; Genentech Inc; South San Francisco CA USA
| |
Collapse
|
21
|
Poornima P, Kumar JD, Zhao Q, Blunder M, Efferth T. Network pharmacology of cancer: From understanding of complex interactomes to the design of multi-target specific therapeutics from nature. Pharmacol Res 2016; 111:290-302. [PMID: 27329331 DOI: 10.1016/j.phrs.2016.06.018] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 12/14/2022]
Abstract
Despite massive investments in drug research and development, the significant decline in the number of new drugs approved or translated to clinical use raises the question, whether single targeted drug discovery is the right approach. To combat complex systemic diseases that harbour robust biological networks such as cancer, single target intervention is proved to be ineffective. In such cases, network pharmacology approaches are highly useful, because they differ from conventional drug discovery by addressing the ability of drugs to target numerous proteins or networks involved in a disease. Pleiotropic natural products are one of the promising strategies due to their multi-targeting and due to lower side effects. In this review, we discuss the application of network pharmacology for cancer drug discovery. We provide an overview of the current state of knowledge on network pharmacology, focus on different technical approaches and implications for cancer therapy (e.g. polypharmacology and synthetic lethality), and illustrate the therapeutic potential with selected examples green tea polyphenolics, Eleutherococcus senticosus, Rhodiola rosea, and Schisandra chinensis). Finally, we present future perspectives on their plausible applications for diagnosis and therapy of cancer.
Collapse
Affiliation(s)
- Paramasivan Poornima
- School of Chemistry, Bangor University, Bangor, Gwynedd LL57 2DG, United Kingdom
| | - Jothi Dinesh Kumar
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - Qiaoli Zhao
- Department of Pharmaceutical Biology, Johannes Gutenberg University, Mainz, Germany
| | - Martina Blunder
- Department of Neuroscience, Biomedical Center, Uppsala University, Uppsala, Sweden and Brain Institute, Federal University of Rio Grande do Norte, UFRN, Natal, Brazil
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Johannes Gutenberg University, Mainz, Germany.
| |
Collapse
|
22
|
Hu G, Li P, Li Y, Wang T, Gao X, Zhang W, Jia G. Methylation levels of P16 and TP53 that are involved in DNA strand breakage of 16HBE cells treated by hexavalent chromium. Toxicol Lett 2016; 249:15-21. [DOI: 10.1016/j.toxlet.2016.03.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/19/2016] [Accepted: 03/07/2016] [Indexed: 01/10/2023]
|
23
|
Krasnov GS, Dmitriev AA, Melnikova NV, Zaretsky AR, Nasedkina TV, Zasedatelev AS, Senchenko VN, Kudryavtseva AV. CrossHub: a tool for multi-way analysis of The Cancer Genome Atlas (TCGA) in the context of gene expression regulation mechanisms. Nucleic Acids Res 2016; 44:e62. [PMID: 26773058 PMCID: PMC4838350 DOI: 10.1093/nar/gkv1478] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/05/2015] [Indexed: 02/07/2023] Open
Abstract
The contribution of different mechanisms to the regulation of gene expression varies for different tissues and tumors. Complementation of predicted mRNA–miRNA and gene–transcription factor (TF) relationships with the results of expression correlation analyses derived for specific tumor types outlines the interactions with functional impact in the current biomaterial. We developed CrossHub software, which enables two-way identification of most possible TF–gene interactions: on the basis of ENCODE ChIP-Seq binding evidence or Jaspar prediction and co-expression according to the data of The Cancer Genome Atlas (TCGA) project, the largest cancer omics resource. Similarly, CrossHub identifies mRNA–miRNA pairs with predicted or validated binding sites (TargetScan, mirSVR, PicTar, DIANA microT, miRTarBase) and strong negative expression correlations. We observed partial consistency between ChIP-Seq or miRNA target predictions and gene–TF/miRNA co-expression, demonstrating a link between these indicators. Additionally, CrossHub expression-methylation correlation analysis can be used to identify hypermethylated CpG sites or regions with the greatest potential impact on gene expression. Thus, CrossHub is capable of outlining molecular portraits of a specific gene and determining the three most common sources of expression regulation: promoter/enhancer methylation, miRNA interference and TF-mediated activation or repression. CrossHub generates formatted Excel workbooks with the detailed results. CrossHub is freely available at https://sourceforge.net/projects/crosshub/.
Collapse
Affiliation(s)
- George S Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia N.N. Blokhin Russian Cancer Research Center, Moscow 115478, Russia Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow 119121, Russia
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Nataliya V Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Andrew R Zaretsky
- M.M. Shemyakin-Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Tatiana V Nasedkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia N.N. Blokhin Russian Cancer Research Center, Moscow 115478, Russia
| | - Alexander S Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia N.N. Blokhin Russian Cancer Research Center, Moscow 115478, Russia
| | - Vera N Senchenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia N.N. Blokhin Russian Cancer Research Center, Moscow 115478, Russia
| |
Collapse
|
24
|
Identification of Gene Expression Pattern Related to Breast Cancer Survival Using Integrated TCGA Datasets and Genomic Tools. BIOMED RESEARCH INTERNATIONAL 2015; 2015:878546. [PMID: 26576432 PMCID: PMC4630377 DOI: 10.1155/2015/878546] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/14/2015] [Accepted: 09/28/2015] [Indexed: 11/18/2022]
Abstract
Several large-scale human cancer genomics projects such as TCGA offered huge genomic and clinical data for researchers to obtain meaningful genomics alterations which intervene in the development and metastasis of the tumor. A web-based TCGA data analysis platform called TCGA4U was developed in this study. TCGA4U provides a visualization solution for this study to illustrate the relationship of these genomics alternations with clinical data. A whole genome screening of the survival related gene expression patterns in breast cancer was studied. The gene list that impacts the breast cancer patient survival was divided into two patterns. Gene list of each of these patterns was separately analyzed on DAVID. The result showed that mitochondrial ribosomes play a more crucial role in the cancer development. We also reported that breast cancer patients with low HSPA2 expression level had shorter overall survival time. This is widely different to findings of HSPA2 expression pattern in other cancer types. TCGA4U provided a new perspective for the TCGA datasets. We believe it can inspire more biomedical researchers to study and explain the genomic alterations in cancer development and discover more targeted therapies to help more cancer patients.
Collapse
|
25
|
Bromberg Y, Capriotti E. VarI-SIG 2014--From SNPs to variants: interpreting different types of genetic variants. BMC Genomics 2015; 16 Suppl 8:I1. [PMID: 26110281 PMCID: PMC4480323 DOI: 10.1186/1471-2164-16-s8-i1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
|