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N Abdel-Aziz N, Y El-Kamah G, A Khairat R, R Mohamed H, Z Gad Y, El-Ghor AM, Amr KS. Mutational spectrum of NF1 gene in 24 unrelated Egyptian families with neurofibromatosis type 1. Mol Genet Genomic Med 2021; 9:e1631. [PMID: 34080803 PMCID: PMC8683698 DOI: 10.1002/mgg3.1631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/19/2020] [Accepted: 02/09/2021] [Indexed: 11/25/2022] Open
Abstract
Background Neurofibromatosis 1 (NF1; OMIM# 162200) is a common autosomal dominant genetic disease [incidence: ~1:3500]. In 95% of cases, clinical diagnosis of the disease is based on the presence of at least two of the seven National Institute of Health diagnostic criteria. The molecular pathology underlying this disorder entails mutation in the NF1 gene. The aim of this study was to investigate clinical and molecular characteristics of a cohort of Egyptian NF1 patients. Method This study included 35 clinically diagnosed NF1 patients descending from 25 unrelated families. Patients had ≥2 NIH diagnostic criteria. Examination of NF1 gene was done through direct cDNA sequencing of multiple overlapping fragments. This was supplemented by NF1 multiple ligation dependent probe amplification (MLPA) analysis of leucocytic DNA. Results The clinical presentations encompassed, café‐au‐lait spots in 100% of probands, freckling (52%), neurofibromas (20%), Lisch nodules of the iris (12%), optic pathway glioma (8%), typical skeletal disorders (20%), and positive family history (32%). Mutations could be detected in 24 families (96%). Eight mutations (33%) were novel. Conclusion This study illustrates the underlying molecular pathology among Egyptian NF1 patients for the first time. It also reports on 8 novel mutation expanding pathogenic mutational spectra in the NF1 gene.
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Affiliation(s)
- Nahla N Abdel-Aziz
- Medical Molecular Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Ghada Y El-Kamah
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Rabab A Khairat
- Medical Molecular Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Hanan R Mohamed
- Zoology Department, Faculty of Science, Cairo University, Cairo, Egypt
| | - Yehia Z Gad
- Medical Molecular Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Akmal M El-Ghor
- Zoology Department, Faculty of Science, Cairo University, Cairo, Egypt
| | - Khalda S Amr
- Medical Molecular Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
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Hart T, Dider S, Han W, Xu H, Zhao Z, Xie L. Toward Repurposing Metformin as a Precision Anti-Cancer Therapy Using Structural Systems Pharmacology. Sci Rep 2016; 6:20441. [PMID: 26841718 PMCID: PMC4740793 DOI: 10.1038/srep20441] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/04/2016] [Indexed: 01/12/2023] Open
Abstract
Metformin, a drug prescribed to treat type-2 diabetes, exhibits anti-cancer effects in a portion of patients, but the direct molecular and genetic interactions leading to this pleiotropic effect have not yet been fully explored. To repurpose metformin as a precision anti-cancer therapy, we have developed a novel structural systems pharmacology approach to elucidate metformin's molecular basis and genetic biomarkers of action. We integrated structural proteome-scale drug target identification with network biology analysis by combining structural genomic, functional genomic, and interactomic data. Through searching the human structural proteome, we identified twenty putative metformin binding targets and their interaction models. We experimentally verified the interactions between metformin and our top-ranked kinase targets. Notably, kinases, particularly SGK1 and EGFR were identified as key molecular targets of metformin. Subsequently, we linked these putative binding targets to genes that do not directly bind to metformin but whose expressions are altered by metformin through protein-protein interactions, and identified network biomarkers of phenotypic response of metformin. The molecular targets and the key nodes in genetic networks are largely consistent with the existing experimental evidence. Their interactions can be affected by the observed cancer mutations. This study will shed new light into repurposing metformin for safe, effective, personalized therapies.
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Affiliation(s)
- Thomas Hart
- The Rockefeller University, New York, New York, United States of America
- Department of Biological Sciences, Hunter College, The City University of New York, New York, New York, United States of America
| | - Shihab Dider
- Department of Biological Sciences, Hunter College, The City University of New York, New York, New York, United States of America
| | - Weiwei Han
- The Key Laboratory for Molecular Enzymology and Engineering, Ministry of Education Jilin University, Changchun, P. R. China
| | - Hua Xu
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Zhongming Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Lei Xie
- Ph.D. Program in Computer Science, Biology, and Biochemistry, The Graduate Center, The City University of New York, New York, New York, United States of America
- Department of Computer Science, Hunter College, The City University of New York, New York, New York, United States of America
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Hart T, Xie L. Providing data science support for systems pharmacology and its implications to drug discovery. Expert Opin Drug Discov 2016; 11:241-56. [PMID: 26689499 DOI: 10.1517/17460441.2016.1135126] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION The conventional one-drug-one-target-one-disease drug discovery process has been less successful in tracking multi-genic, multi-faceted complex diseases. Systems pharmacology has emerged as a new discipline to tackle the current challenges in drug discovery. The goal of systems pharmacology is to transform huge, heterogeneous, and dynamic biological and clinical data into interpretable and actionable mechanistic models for decision making in drug discovery and patient treatment. Thus, big data technology and data science will play an essential role in systems pharmacology. AREAS COVERED This paper critically reviews the impact of three fundamental concepts of data science on systems pharmacology: similarity inference, overfitting avoidance, and disentangling causality from correlation. The authors then discuss recent advances and future directions in applying the three concepts of data science to drug discovery, with a focus on proteome-wide context-specific quantitative drug target deconvolution and personalized adverse drug reaction prediction. EXPERT OPINION Data science will facilitate reducing the complexity of systems pharmacology modeling, detecting hidden correlations between complex data sets, and distinguishing causation from correlation. The power of data science can only be fully realized when integrated with mechanism-based multi-scale modeling that explicitly takes into account the hierarchical organization of biological systems from nucleic acid to proteins, to molecular interaction networks, to cells, to tissues, to patients, and to populations.
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Affiliation(s)
- Thomas Hart
- a The Rockefeller University , New York , NY , USA.,b Department of Biological Sciences, Hunter College , The City University of New York , New York , NY , USA
| | - Lei Xie
- c Department of Computer Science, Hunter College , The City University of New York , New York , NY , USA.,d The Graduate Center , The City University of New York , New York , NY , USA
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Jha AR, Zhou D, Brown CD, Kreitman M, Haddad GG, White KP. Shared Genetic Signals of Hypoxia Adaptation in Drosophila and in High-Altitude Human Populations. Mol Biol Evol 2015; 33:501-17. [PMID: 26576852 PMCID: PMC4866538 DOI: 10.1093/molbev/msv248] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The ability to withstand low oxygen (hypoxia tolerance) is a polygenic and mechanistically conserved trait that has important implications for both human health and evolution. However, little is known about the diversity of genetic mechanisms involved in hypoxia adaptation in evolving populations. We used experimental evolution and whole-genome sequencing in Drosophila melanogaster to investigate the role of natural variation in adaptation to hypoxia. Using a generalized linear mixed model we identified significant allele frequency differences between three independently evolved hypoxia-tolerant populations and normoxic control populations for approximately 3,800 single nucleotide polymorphisms. Around 50% of these variants are clustered in 66 distinct genomic regions. These regions contain genes that are differentially expressed between hypoxia-tolerant and normoxic populations and several of the differentially expressed genes are associated with metabolic processes. Additional genes associated with respiratory and open tracheal system development also show evidence of directional selection. RNAi-mediated knockdown of several candidate genes’ expression significantly enhanced survival in severe hypoxia. Using genomewide single nucleotide polymorphism data from four high-altitude human populations—Sherpas, Tibetans, Ethiopians, and Andeans, we found that several human orthologs of the genes under selection in flies are also likely under positive selection in all four high-altitude human populations. Thus, our results indicate that selection for hypoxia tolerance can act on standing genetic variation in similar genes and pathways present in organisms diverged by hundreds of millions of years.
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Affiliation(s)
- Aashish R Jha
- Institute for Genomics and Systems Biology, The University of Chicago Department of Human Genetics, The University of Chicago Department of Ecology and Evolution, The University of Chicago
| | - Dan Zhou
- Division of Respiratory Medicine, Department of Pediatrics, University of California at San Diego
| | - Christopher D Brown
- Institute for Genomics and Systems Biology, The University of Chicago Department of Human Genetics, The University of Chicago
| | - Martin Kreitman
- Institute for Genomics and Systems Biology, The University of Chicago Department of Ecology and Evolution, The University of Chicago Committee on Genetics, Genomics and Systems Biology, The University of Chicago
| | - Gabriel G Haddad
- Division of Respiratory Medicine, Department of Pediatrics, University of California at San Diego Department of Neurosciences, University of California at San Diego Rady Children's Hospital, San Diego, CA
| | - Kevin P White
- Institute for Genomics and Systems Biology, The University of Chicago Department of Human Genetics, The University of Chicago Department of Ecology and Evolution, The University of Chicago Committee on Genetics, Genomics and Systems Biology, The University of Chicago
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Xie L, Ge X, Tan H, Xie L, Zhang Y, Hart T, Yang X, Bourne PE. Towards structural systems pharmacology to study complex diseases and personalized medicine. PLoS Comput Biol 2014; 10:e1003554. [PMID: 24830652 PMCID: PMC4022462 DOI: 10.1371/journal.pcbi.1003554] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Genome-Wide Association Studies (GWAS), whole genome sequencing, and high-throughput omics techniques have generated vast amounts of genotypic and molecular phenotypic data. However, these data have not yet been fully explored to improve the effectiveness and efficiency of drug discovery, which continues along a one-drug-one-target-one-disease paradigm. As a partial consequence, both the cost to launch a new drug and the attrition rate are increasing. Systems pharmacology and pharmacogenomics are emerging to exploit the available data and potentially reverse this trend, but, as we argue here, more is needed. To understand the impact of genetic, epigenetic, and environmental factors on drug action, we must study the structural energetics and dynamics of molecular interactions in the context of the whole human genome and interactome. Such an approach requires an integrative modeling framework for drug action that leverages advances in data-driven statistical modeling and mechanism-based multiscale modeling and transforms heterogeneous data from GWAS, high-throughput sequencing, structural genomics, functional genomics, and chemical genomics into unified knowledge. This is not a small task, but, as reviewed here, progress is being made towards the final goal of personalized medicines for the treatment of complex diseases.
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Affiliation(s)
- Lei Xie
- Department of Computer Science, Hunter College, The City University of New York, New York, New York, United States of America
- Ph.D. Program in Computer Science, Biology, and Biochemistry, The Graduate Center, The City University of New York, New York, New York, United States of America
- * E-mail:
| | - Xiaoxia Ge
- Department of Computer Science, Hunter College, The City University of New York, New York, New York, United States of America
| | - Hepan Tan
- Department of Computer Science, Hunter College, The City University of New York, New York, New York, United States of America
| | - Li Xie
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Yinliang Zhang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Thomas Hart
- Department of Biological Sciences, Hunter College, The City University of New York, New York, New York, United States of America
| | - Xiaowei Yang
- School of Public Health, Hunter College, The City University of New York, New York, New York, United States of America
| | - Philip E. Bourne
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
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Bromberg Y, Capriotti E. Thoughts from SNP-SIG 2012: future challenges in the annotation of genetic variations. BMC Genomics 2013; 14 Suppl 3:S1. [PMID: 23819751 PMCID: PMC3665538 DOI: 10.1186/1471-2164-14-s3-s1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA.
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