1
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Shen-Gunther J, Easley A. HPV, HBV, and HIV-1 Viral Integration Site Mapping: A Streamlined Workflow from NGS to Genomic Insights of Carcinogenesis. Viruses 2024; 16:975. [PMID: 38932267 PMCID: PMC11209625 DOI: 10.3390/v16060975] [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: 05/27/2024] [Revised: 06/14/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024] Open
Abstract
Viral integration within the host genome plays a pivotal role in carcinogenesis. Various disruptive mechanisms are involved, leading to genomic instability, mutations, and DNA damage. With next-generation sequencing (NGS), we can now precisely identify viral and host genomic breakpoints and chimeric sequences, which are useful for integration site analysis. In this study, we evaluated a commercial hybrid capture NGS panel specifically designed for detecting three key viruses: HPV, HBV, and HIV-1. We also tested workflows for Viral Hybrid Capture (VHC) and Viral Integration Site (VIS) analysis, leveraging customized viral databases in CLC Microbial Genomics. By analyzing sequenced data from virally infected cancer cell lines (including SiHa, HeLa, CaSki, C-33A, DoTc2, 2A3, SCC154 for HPV; 3B2, SNU-182 for HBV; and ACH-2 for HIV-1), we precisely pinpointed viral integration sites. The workflow also highlighted disrupted and neighboring human genes that may play a crucial role in tumor development. Our results included informative virus-host read mappings, genomic breakpoints, and integration circular plots. These visual representations enhance our understanding of the integration process. In conclusion, our seamless end-to-end workflow bridges the gap in understanding viral contributions to cancer development, paving the way for improved diagnostics and treatment strategies.
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Affiliation(s)
- Jane Shen-Gunther
- Gynecologic Oncology & Clinical Investigation, Department of Clinical Investigation, Brooke Army Medical Center, San Antonio, TX 78234, USA
| | - Acarizia Easley
- Department of Clinical Investigation, Brooke Army Medical Center, San Antonio, TX 78234, USA;
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2
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Galati L, Chiantore MV, Marinaro M, Di Bonito P. Human Oncogenic Viruses: Characteristics and Prevention Strategies-Lessons Learned from Human Papillomaviruses. Viruses 2024; 16:416. [PMID: 38543781 PMCID: PMC10974567 DOI: 10.3390/v16030416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 05/23/2024] Open
Abstract
Approximately 12% of human cancers worldwide are associated with infectious agents, which are classified by the International Agency for Research on Cancer (IARC) as Group 1 within the agents that are carcinogenic to humans. Most of these agents are viruses. Group 1 oncogenic viruses include hepatitis C virus, hepatitis B virus (HBV), human T-cell lymphotropic virus type 1, Epstein-Barr virus, Kaposi sarcoma-associated herpesvirus, human immunodeficiency virus-1 and high-risk human papillomaviruses (HPVs). In addition, some human polyomaviruses are suspected of inducing cancer prevalently in hosts with impaired immune responses. Merkel cell polyomavirus has been associated with Merkel cell carcinoma and included by the IARC in Group 2A (i.e., probably carcinogenic to humans). Linking viruses to human cancers has allowed for the development of diagnostic, prophylactic and therapeutic measures. Vaccination significantly reduced tumours induced by two oncogenic viruses as follows: HBV and HPV. Herein, we focus on mucosal alpha HPVs, which are responsible for the highest number of cancer cases due to tumour viruses and against which effective prevention strategies have been developed to reduce the global burden of HPV-related cancers.
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Affiliation(s)
- Luisa Galati
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy;
| | - Maria Vincenza Chiantore
- Department of Infectious Diseases, Viral Hepatitis and Oncovirus and Retrovirus Diseases (EVOR) Unit, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy;
| | - Mariarosaria Marinaro
- Department of Infectious Diseases, Microorganisms and Host Response: Research and Technological Innovation (MICROS) Unit, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy;
| | - Paola Di Bonito
- Department of Infectious Diseases, Viral Hepatitis and Oncovirus and Retrovirus Diseases (EVOR) Unit, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy;
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3
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Minarovits J. Human tumor viruses: induction of three-dimensional alterations in the host genome structure. Front Microbiol 2023; 14:1280210. [PMID: 37928671 PMCID: PMC10620758 DOI: 10.3389/fmicb.2023.1280210] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 09/21/2023] [Indexed: 11/07/2023] Open
Abstract
Certain viruses called tumor viruses or oncoviruses are capable to change the gene expression pattern of distinct human or animal cell types in tissue culture, resulting in uncontrolled proliferation as well as a change in the social behavior of the infected cells: the oncovirus-transformed, immortalized cells are capable to form malignant neoplasms in suitable animal models. At present, seven human viruses are categorized as causative agents of distinct human malignancies. The genomes of human tumor viruses, typically encode viral oncoproteins and non- translated viral RNAs that affect the gene expression pattern of their target cells or induce genetic and epigenetic alterations contributing to oncogenesis. Recently, the application of chromatin conformation capture technologies and three-dimensional (3D) molecular imaging techniques revealed how the gene products or genomes of certain human tumor viruses interact with and induce alterations in the 3D host genome structure. This Mini Review aims to cover selected aspects of these developments. The papers, discussed briefly, describe how insertion of a novel viral binding site for the 3D genome organizer cellular protein CCCTC-binding factor (CTCF) into the DNA of T cells infected by human T-cell lymphotropic virus type 1 (HTLV-1) may contribute to lymphomagenesis, as well as how integration of high risk human papillomavirus genome into the host cell DNA may facilitate cervical carcinogenesis. Recent results regarding the interactions of cellular genomes with the episomal, chromatinized DNA genomes of oncogenic human herpesvirus, Epstein-Barr virus (EBV) will also be summarized, similarly to available data regarding contacts formed by episomal or integrated hepatitis B virus (HBV) DNA with host chromatin. Finally, a putative mechanism of hepatitis C virus (HCV) induced chromatin alterations will be presented, which may solve the riddle, how a cytoplasmic RNA virus without a viral oncogene could induce malingnant transfrormation of hepatocytes.
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Affiliation(s)
- Janos Minarovits
- Department of Oral Biology and Experimental Dental Research, Faculty of Dentistry, University of Szeged, Szeged, Hungary
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4
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Zastawna B, Milewska A, Załuska R, Kozłowski R, Zastawna M, Marczak M. Analysis of Parents' Attitudes and Knowledge toward Immunization and How These Factors Influence Their Decisions to Vaccinate Their Children against Human Papilloma Virus (HPV). MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1755. [PMID: 37893473 PMCID: PMC10608555 DOI: 10.3390/medicina59101755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023]
Abstract
Background and objectives: Vaccination hesitancy is a growing problem associated with decreasing chances for the elimination of vaccine-preventable diseases through immunization. This research was conducted to learn about parents' attitudes toward vaccination, particularly against HPV, in the context of their beliefs and fears regarding immunization and the impact of these views on their children's vaccination decisions. An additional goal was to determine what views or convictions most often lead to the phenomenon of delaying or refusing vaccinations, especially HPV vaccines, in the surveyed community. Materials and Methods: An online questionnaire was conducted in which parents marked how they vaccinated their children with mandatory vaccinations and whether they took the opportunity to protect their children with additional vaccinations, including HPV and COVID-19. Respondents also marked the extent to which they agreed with the statements, regarding the safety of vaccinations, doubts about them, as well as popular anti-vaccine myths. Results: A total of 250 questionnaires were collected with data on the immunization of 425 children. Associations between specific beliefs and vaccine abstention were established. The most motivating factor for vaccination against HPV was the parent's awareness that the virus HP is the cause of cancer. The most inhibiting factor was respondent's compliance with the opinion that HPV vaccines can affect the child's sexual activity. Conclusions: The results indicate that information campaigns are needed, especially focusing on vaccine safety and the regularity and transparency of monitoring adverse effects. The obtained results will be used to create educational interventions against vaccination hesitancy more adapted to local conditions.
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Affiliation(s)
- Beata Zastawna
- Department of Management and Logistics in Health Care, Medical University of Lodz, 90-131 Lodz, Poland; (R.Z.); (R.K.)
| | - Anna Milewska
- Department of Statistics and Medical Informatics, Medical University of Bialystok, 15-089 Bialystok, Poland;
| | - Roman Załuska
- Department of Management and Logistics in Health Care, Medical University of Lodz, 90-131 Lodz, Poland; (R.Z.); (R.K.)
| | - Remigiusz Kozłowski
- Department of Management and Logistics in Health Care, Medical University of Lodz, 90-131 Lodz, Poland; (R.Z.); (R.K.)
| | - Martyna Zastawna
- Department of Psychology, SWPS University of Social Sciences and Humanities, 03-815 Warsaw, Poland;
| | - Michał Marczak
- Collegium of Management, WSB University in Warsaw, 03-204 Warsaw, Poland
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5
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Diakite M, Shaw-Saliba K, Lau CY. Malignancy and viral infections in Sub-Saharan Africa: A review. FRONTIERS IN VIROLOGY (LAUSANNE, SWITZERLAND) 2023; 3:1103737. [PMID: 37476029 PMCID: PMC10358275 DOI: 10.3389/fviro.2023.1103737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
The burden of malignancy related to viral infection is increasing in Sub-Saharan Africa (SSA). In 2018, approximately 2 million new cancer cases worldwide were attributable to infection. Prevention or treatment of these infections could reduce cancer cases by 23% in less developed regions and about 7% in developed regions. Contemporaneous increases in longevity and changes in lifestyle have contributed to the cancer burden in SSA. African hospitals are reporting more cases of cancer related to infection (e.g., cervical cancer in women and stomach and liver cancer in men). SSA populations also have elevated underlying prevalence of viral infections compared to other regions. Of 10 infectious agents identified as carcinogenic by the International Agency for Research on Cancer, six are viruses: hepatitis B and C viruses (HBV and HCV, respectively), Epstein-Barr virus (EBV), high-risk types of human papillomavirus (HPV), Human T-cell lymphotropic virus type 1 (HTLV-1), and Kaposi's sarcoma herpesvirus (KSHV, also known as human herpesvirus type 8, HHV-8). Human immunodeficiency virus type 1 (HIV) also facilitates oncogenesis. EBV is associated with lymphomas and nasopharyngeal carcinoma; HBV and HCV are associated with hepatocellular carcinoma; KSHV causes Kaposi's sarcoma; HTLV-1 causes T-cell leukemia and lymphoma; HPV causes carcinoma of the oropharynx and anogenital squamous cell cancer. HIV-1, for which SSA has the greatest global burden, has been linked to increasing risk of malignancy through immunologic dysregulation and clonal hematopoiesis. Public health approaches to prevent infection, such as vaccination, safer injection techniques, screening of blood products, antimicrobial treatments and safer sexual practices could reduce the burden of cancer in Africa. In SSA, inequalities in access to cancer screening and treatment are exacerbated by the perception of cancer as taboo. National level cancer registries, new screening strategies for detection of viral infection and public health messaging should be prioritized in SSA's battle against malignancy. In this review, we discuss the impact of carcinogenic viruses in SSA with a focus on regional epidemiology.
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Affiliation(s)
- Mahamadou Diakite
- University Clinical Research Center, University of Sciences, Techniques, and Technologies, Bamako, Mali
| | - Kathryn Shaw-Saliba
- Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Chuen-Yen Lau
- HIV Dynamics and Replication Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, United States
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6
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Glimmers of hope for targeting oncogenic KRAS-G12D. Cancer Gene Ther 2023; 30:391-393. [PMID: 36414681 DOI: 10.1038/s41417-022-00561-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022]
Abstract
KRAS mutations are one of the most common genetic abnormalities in cancer, especially lung, colon, and pancreatic cancers. Strategies targeting the oncogenic KRAS pathway include direct and indirect approaches. KRAS-G12C inhibitors developed based on binding to the switch II pocket structure of KRAS mutant protein represent a breakthrough in the development of targeted therapeutic strategies against oncogenic proteins previously considered undruggable. The covalent KRAS-G12C inhibitors sotorasib (AMG510) and adagrasib (MRTX849) are used to treat patients with KRAS-G12C-mutated non-small cell lung cancer. Emerging research shows that other host point mutations in KRAS can also be directly targeted by small-molecule compounds. Recently, through extensive structure-based drug design from Mirati Therapeutics, a novel non-covalent KRAS-G12D inhibitor, MRTX1133, showed significant preclinical antitumor activity in KRAS-G12D-bearing tumor cells, especially pancreatic ductal adenocarcinoma. Here, we discuss the selectivity, efficacy, toxicity, and potential application challenges of this novel targeted protein inhibitor.
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7
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Weber LI, Hartl M. Strategies to target the cancer driver MYC in tumor cells. Front Oncol 2023; 13:1142111. [PMID: 36969025 PMCID: PMC10032378 DOI: 10.3389/fonc.2023.1142111] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 02/10/2023] [Indexed: 03/29/2023] Open
Abstract
The MYC oncoprotein functions as a master regulator of cellular transcription and executes non-transcriptional tasks relevant to DNA replication and cell cycle regulation, thereby interacting with multiple proteins. MYC is required for fundamental cellular processes triggering proliferation, growth, differentiation, or apoptosis and also represents a major cancer driver being aberrantly activated in most human tumors. Due to its non-enzymatic biochemical functions and largely unstructured surface, MYC has remained difficult for specific inhibitor compounds to directly address, and consequently, alternative approaches leading to indirect MYC inhibition have evolved. Nowadays, multiple organic compounds, nucleic acids, or peptides specifically interfering with MYC activities are in preclinical or early-stage clinical studies, but none of them have been approved so far for the pharmacological treatment of cancer patients. In addition, specific and efficient delivery technologies to deliver MYC-inhibiting agents into MYC-dependent tumor cells are just beginning to emerge. In this review, an overview of direct and indirect MYC-inhibiting agents and their modes of MYC inhibition is given. Furthermore, we summarize current possibilities to deliver appropriate drugs into cancer cells containing derailed MYC using viral vectors or appropriate nanoparticles. Finding the right formulation to target MYC-dependent cancers and to achieve a high intracellular concentration of compounds blocking or attenuating oncogenic MYC activities could be as important as the development of novel MYC-inhibiting principles.
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8
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Wei C, Li H. Benzothiazole Derivatives Targeting G‐Quadruplex DNA: Synthesis, DNA Interaction and Living Cell Imaging. ChemistrySelect 2022. [DOI: 10.1002/slct.202202565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Chunying Wei
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science Shanxi University Taiyuan 030006 P. R. China
| | - Haiying Li
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science Shanxi University Taiyuan 030006 P.R. China
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9
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Appraisal for the Potential of Viral and Nonviral Vectors in Gene Therapy: A Review. Genes (Basel) 2022; 13:genes13081370. [PMID: 36011281 PMCID: PMC9407213 DOI: 10.3390/genes13081370] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/24/2022] [Accepted: 07/26/2022] [Indexed: 12/16/2022] Open
Abstract
Over the past few decades, gene therapy has gained immense importance in medical research as a promising treatment strategy for diseases such as cancer, AIDS, Alzheimer’s disease, and many genetic disorders. When a gene needs to be delivered to a target cell inside the human body, it has to pass a large number of barriers through the extracellular and intracellular environment. This is why the delivery of naked genes and nucleic acids is highly unfavorable, and gene delivery requires suitable vectors that can carry the gene cargo to the target site and protect it from biological degradation. To date, medical research has come up with two types of gene delivery vectors, which are viral and nonviral vectors. The ability of viruses to protect transgenes from biological degradation and their capability to efficiently cross cellular barriers have allowed gene therapy research to develop new approaches utilizing viruses and their different genomes as vectors for gene delivery. Although viral vectors are very efficient, science has also come up with numerous nonviral systems based on cationic lipids, cationic polymers, and inorganic particles that provide sustainable gene expression without triggering unwanted inflammatory and immune reactions, and that are considered nontoxic. In this review, we discuss in detail the latest data available on all viral and nonviral vectors used in gene delivery. The mechanisms of viral and nonviral vector-based gene delivery are presented, and the advantages and disadvantages of all types of vectors are also given.
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10
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Rezende Miranda R, Zhang C. Reactivity-based chemical-genetic study of protein kinases. RSC Med Chem 2022; 13:783-797. [PMID: 35923719 PMCID: PMC9298188 DOI: 10.1039/d1md00389e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/28/2022] [Indexed: 11/21/2022] Open
Abstract
The human protein kinase superfamily comprises over 500 members that operate in nearly every signal transduction pathway and regulate essential cellular processes. Deciphering the functional roles of protein kinases with small-molecule inhibitors is essential to enhance our understanding of cell signaling and to facilitate the development of new therapies. However, it is rather challenging to identify selective kinase inhibitors because of the conserved nature of the ATP binding site. A number of chemical-genetic approaches have been developed during the past two decades to enable selective chemical perturbation of the activity of individual kinases. Herein, we review the development and application of chemical-genetic strategies that feature the use of covalent inhibitors targeting cysteine residues to dissect the cellular functions of protein kinases.
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Affiliation(s)
- Renata Rezende Miranda
- Department of Chemistry, Loker Hydrocarbon Research Institute, University of Southern California Los Angeles California 90089 USA
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology Rochester New York 14623 USA
| | - Chao Zhang
- Department of Chemistry, Loker Hydrocarbon Research Institute, University of Southern California Los Angeles California 90089 USA
- USC Norris Comprehensive Cancer Center, University of Southern California Los Angeles California 90089 USA
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11
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Alexa A, Sok P, Gross F, Albert K, Kobori E, Póti ÁL, Gógl G, Bento I, Kuang E, Taylor SS, Zhu F, Ciliberto A, Reményi A. A non-catalytic herpesviral protein reconfigures ERK-RSK signaling by targeting kinase docking systems in the host. Nat Commun 2022; 13:472. [PMID: 35078976 PMCID: PMC8789800 DOI: 10.1038/s41467-022-28109-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 01/07/2022] [Indexed: 12/16/2022] Open
Abstract
The Kaposi's sarcoma associated herpesvirus protein ORF45 binds the extracellular signal-regulated kinase (ERK) and the p90 Ribosomal S6 kinase (RSK). ORF45 was shown to be a kinase activator in cells but a kinase inhibitor in vitro, and its effects on the ERK-RSK complex are unknown. Here, we demonstrate that ORF45 binds ERK and RSK using optimized linear binding motifs. The crystal structure of the ORF45-ERK2 complex shows how kinase docking motifs recognize the activated form of ERK. The crystal structure of the ORF45-RSK2 complex reveals an AGC kinase docking system, for which we provide evidence that it is functional in the host. We find that ORF45 manipulates ERK-RSK signaling by favoring the formation of a complex, in which activated kinases are better protected from phosphatases and docking motif-independent RSK substrate phosphorylation is selectively up-regulated. As such, our data suggest that ORF45 interferes with the natural design of kinase docking systems in the host.
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Affiliation(s)
- Anita Alexa
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Péter Sok
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Fridolin Gross
- IFOM, Istituto FIRC di Oncologia Molecolare, 20139, Milan, Italy
| | - Krisztián Albert
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Evan Kobori
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0654, USA
| | - Ádám L Póti
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Gergő Gógl
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary
| | - Isabel Bento
- European Molecular Biology Laboratory, Hamburg, Germany
| | - Ersheng Kuang
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306-4370, USA
| | - Susan S Taylor
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, San Diego, CA, 92093-0654, USA
| | - Fanxiu Zhu
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306-4370, USA
| | - Andrea Ciliberto
- IFOM, Istituto FIRC di Oncologia Molecolare, 20139, Milan, Italy
| | - Attila Reményi
- Biomolecular Interactions Research Group, Institute of Organic Chemistry, Research Center for Natural Sciences, H-1117, Budapest, Hungary.
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12
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Chia J, Wang SC, Wee S, Gill DJ, Tay F, Kannan S, Verma CS, Gunaratne J, Bard FA. Src activates retrograde membrane traffic through phosphorylation of GBF1. eLife 2021; 10:68678. [PMID: 34870592 PMCID: PMC8727025 DOI: 10.7554/elife.68678] [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: 03/23/2021] [Accepted: 12/05/2021] [Indexed: 12/14/2022] Open
Abstract
The Src tyrosine kinase controls cancer-critical protein glycosylation through Golgi to ER relocation of GALNTs enzymes. How Src induces this trafficking event is unknown. Golgi to ER transport depends on the GTP exchange factor (GEF) GBF1 and small GTPase Arf1. Here, we show that Src induces the formation of tubular transport carriers containing GALNTs. The kinase phosphorylates GBF1 on 10 tyrosine residues; two of them, Y876 and Y898, are located near the C-terminus of the Sec7 GEF domain. Their phosphorylation promotes GBF1 binding to the GTPase; molecular modeling suggests partial melting of the Sec7 domain and intramolecular rearrangement. GBF1 mutants defective for these rearrangements prevent binding, carrier formation, and GALNTs relocation, while phosphomimetic GBF1 mutants induce tubules. In sum, Src promotes GALNTs relocation by promoting GBF1 binding to Arf1. Based on residue conservation, similar regulation of GEF-Arf complexes by tyrosine phosphorylation could be a conserved and widespread mechanism.
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Affiliation(s)
- Joanne Chia
- Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Shyi-Chyi Wang
- Institute of Molecular and Cell Biology, Singapore, Singapore.,Institute of Bioengineering and Bioimaging, Singapore, Singapore
| | - Sheena Wee
- Institute of Molecular and Cell Biology, Singapore, Singapore
| | | | - Felicia Tay
- Institute of Molecular and Cell Biology, Singapore, Singapore
| | | | - Chandra S Verma
- Bioinformatics Institute, Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | | | - Frederic A Bard
- Institute of Molecular and Cell Biology, Singapore, Singapore
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13
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Bono LM, Mao S, Done RE, Okamoto KW, Chan BK, Turner PE. Advancing phage therapy through the lens of virus host-breadth and emergence potential. Adv Virus Res 2021; 111:63-110. [PMID: 34663499 DOI: 10.1016/bs.aivir.2021.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Phages are viruses that specifically infect bacteria, and their biodiversity contributes to historical and current development of phage therapy to treat myriad bacterial infections. Phage therapy holds promise as an alternative to failing chemical antibiotics, but there are benefits and costs of this technology. Here, we review the rich history of phage therapy, highlighting reasons (often political) why it was widely rejected by Western medicine until recently. One longstanding idea involves mixing different phages together in cocktails, to increase the probability of killing target pathogenic bacteria without pre-screening for phage susceptibility. By challenging 30 lytic phages to infect 14 strains of the bacteria Pseudomonas aeruginosa, we showed that some phages were "generalists" with broad host-ranges, emphasizing that extreme host-specificity of phages was not necessarily a liability. Using a "greedy algorithm" analysis, we identified the best cocktail mixture of phages to achieve broad bacteria killing. Additionally, we review how virus host-range can evolve and connect lessons learned from virus emergence-including contributions of elevated virus mutation rates in promoting emergence and virus evolutionary transitions from specialized to generalized host-use-as cautionary tales for avoiding risk of "off-target" phage emergence on commensal bacteria in microbiomes. Throughout, we highlight how fundamental understanding of virus ecology and evolution is vital for developing phage therapy; heeding these principles should help in designing therapeutic strategies that do not recapitulate consequences of virus selection to emerge on novel hosts.
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Affiliation(s)
- Lisa M Bono
- Department of Biology, Emory University, Atlanta, GA, United States.
| | - Stephanie Mao
- Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Rachel E Done
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, GA, United States; Division of Pulmonary, Allergy and Immunology, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
| | - Kenichi W Okamoto
- Department of Biology, University of St. Thomas, St. Paul, MN, United States
| | - Benjamin K Chan
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States; Microbiology Program, Yale School of Medicine, New Haven, CT, United States
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14
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Ashrafi F, Ghezeldasht SA, Ghobadi MZ. Identification of joint gene players implicated in the pathogenesis of HTLV-1 and BLV through a comprehensive system biology analysis. Microb Pathog 2021; 160:105153. [PMID: 34419613 DOI: 10.1016/j.micpath.2021.105153] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 08/10/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Human T-cell lymphotropic virus type 1 (HTLV-1) and bovine leukemia virus (BLV) are oncogenic viruses that induce adult T cell leukemia/lymphoma (ATLL) and enzootic bovine leukosis (EBL), respectively. HTLV-1 principally infects CD4+ T cells comprising regulatory T cells (Tregs), T helper 1 (Th1), and T helper 2 (Th2), while BLV infects B lymphocytes. Both viruses may impel cell proliferation and malignancy. METHODS To survey the transcriptomic variations due to HTLV-1 and BLV infection and further hematologic malignancies, differential expression genes (DEGs) were explored between leukemia and normal samples using the DESeq2 package. Gene set enrichment analyses (GSEA) were then performed to identify significant gene sets using the FGSEA package. Afterward, the protein-protein interaction (PPI) networks were reconstructed using the STRING online database. Eventually, the hub significant genes and modules were determined through network analysis and MCODE algorithm, respectively. RESULTS Our results uncloaked that four common functional gene sets including mitotic-spindle, G2M-checkpoint, E2F-targets, and MYC-targets-V1 are involved in the human and ovine hosts. Furthermore, twelve up-regulated hub genes including BIRC5, CCNA2, CCNB2, BUB1, DLGAP5, TOP2A, PBK, ASPM, UBE2C, CEP55, KIF20A, and NUSAP1 were identified which were similarly activated in both human and ovine hosts. They mostly participate in pathways including cell cycle, cell division, DNA damage responses, growth factors production, and p53 signaling pathway. The dysregulated hub genes and pathways seem to be involved in the development and progression of the infected cells toward malignancy. CONCLUSION There is common gene groups between HTLV-1 and BLV infections that promote viral malignancy through enhancing cell proliferation and overall survival of cancer cells. The dysregulated genes and pathways may be the efficient candidates for the therapy of the mentioned life-threatening diseases.
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Affiliation(s)
- Fereshteh Ashrafi
- Department of Animal Science, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Sanaz Ahmadi Ghezeldasht
- Inflammation and Inflammatory Diseases Division, Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohadeseh Zarei Ghobadi
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran; Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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15
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Paudel R, Fusi L, Schmidt M. The MEK5/ERK5 Pathway in Health and Disease. Int J Mol Sci 2021; 22:ijms22147594. [PMID: 34299213 PMCID: PMC8303459 DOI: 10.3390/ijms22147594] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 12/12/2022] Open
Abstract
The MEK5/ERK5 mitogen-activated protein kinases (MAPK) cascade is a unique signaling module activated by both mitogens and stress stimuli, including cytokines, fluid shear stress, high osmolarity, and oxidative stress. Physiologically, it is mainly known as a mechanoreceptive pathway in the endothelium, where it transduces the various vasoprotective effects of laminar blood flow. However, it also maintains integrity in other tissues exposed to mechanical stress, including bone, cartilage, and muscle, where it exerts a key function as a survival and differentiation pathway. Beyond its diverse physiological roles, the MEK5/ERK5 pathway has also been implicated in various diseases, including cancer, where it has recently emerged as a major escape route, sustaining tumor cell survival and proliferation under drug stress. In addition, MEK5/ERK5 dysfunction may foster cardiovascular diseases such as atherosclerosis. Here, we highlight the importance of the MEK5/ERK5 pathway in health and disease, focusing on its role as a protective cascade in mechanical stress-exposed healthy tissues and its function as a therapy resistance pathway in cancers. We discuss the perspective of targeting this cascade for cancer treatment and weigh its chances and potential risks when considering its emerging role as a protective stress response pathway.
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16
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Amere Subbarao S. Cancer vs. SARS-CoV-2 induced inflammation, overlapping functions, and pharmacological targeting. Inflammopharmacology 2021; 29:343-366. [PMID: 33723711 PMCID: PMC7959277 DOI: 10.1007/s10787-021-00796-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/27/2021] [Indexed: 12/15/2022]
Abstract
Inflammation is an intrinsic defence mechanism triggered by the immune system against infection or injury. Chronic inflammation allows the host to recover or adapt through cellular and humoral responses, whereas acute inflammation leads to cytokine storms resulting in tissue damage. In this review, we present the overlapping outcomes of cancer inflammation with virus-induced inflammation. The study emphasises how anti-inflammatory drugs that work against cancer inflammation may work against the inflammation caused by the viral infection. It is established that the cytokine storm induced in response to SARS-CoV-2 infection contributes to disease-associated mortality. While cancer remains the second among the diseases associated with mortality worldwide, cancer patients' mortality rates are often observed upon extended periods after illness, usually ranging from months to years. However, the mortality rates associated with COVID-19 disease are robust. The cytokine storm induced by SARS-CoV-2 infection appeared to be responsible for the multi-organ failure and increased mortality rates. Since both cancer and COVID-19 disease share overlapping inflammatory mechanisms, repurposing some anticancer and anti-inflammatory drugs for COVID-19 may lower mortality rates. Here, we review some of these inflammatory mechanisms and propose some potential chemotherapeutic agents to intervene in them. We also discuss the repercussions of anti-inflammatory drugs such as glucocorticoids and hydroxychloroquine with zinc or antiviral drugs such as ivermectin and remdesivir against SARS-CoV-2 induced cytokine storm. In this review, we emphasise on various possibilities to reduce SARS-CoV-2 induced cytokine storm.
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17
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Yuki R, Hagino M, Ueno S, Kuga T, Saito Y, Fukumoto Y, Yamaguchi N, Yamaguchi N, Nakayama Y. The tyrosine kinase v-Src modifies cytotoxicities of anticancer drugs targeting cell division. J Cell Mol Med 2021; 25:1677-1687. [PMID: 33465289 PMCID: PMC7875926 DOI: 10.1111/jcmm.16270] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 12/11/2022] Open
Abstract
v-Src oncogene causes cell transformation through its strong tyrosine kinase activity. We have revealed that v-Src-mediated cell transformation occurs at a low frequency and it is attributed to mitotic abnormalities-mediated chromosome instability. v-Src directly phosphorylates Tyr-15 of cyclin-dependent kinase 1 (CDK1), thereby causing mitotic slippage and reduction in Eg5 inhibitor cytotoxicity. However, it is not clear whether v-Src modifies cytotoxicities of the other anticancer drugs targeting cell division. In this study, we found that v-Src restores cancer cell viability reduced by various microtubule-targeting agents (MTAs), although v-Src does not alter cytotoxicity of DNA-damaging anticancer drugs. v-Src causes mitotic slippage of MTAs-treated cells, consequently generating proliferating tetraploid cells. We further demonstrate that v-Src also restores cell viability reduced by a polo-like kinase 1 (PLK1) inhibitor. Interestingly, treatment with Aurora kinase inhibitor strongly induces cell death when cells express v-Src. These results suggest that the v-Src modifies cytotoxicities of anticancer drugs targeting cell division. Highly activated Src-induced resistance to MTAs through mitotic slippage might have a risk to enhance the malignancy of cancer cells through the increase in chromosome instability upon chemotherapy using MTAs.
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Affiliation(s)
- Ryuzaburo Yuki
- Department of Biochemistry and Molecular BiologyKyoto Pharmaceutical UniversityKyotoJapan
| | - Mari Hagino
- Department of Biochemistry and Molecular BiologyKyoto Pharmaceutical UniversityKyotoJapan
| | - Sachi Ueno
- Department of Biochemistry and Molecular BiologyKyoto Pharmaceutical UniversityKyotoJapan
| | - Takahisa Kuga
- Department of Biochemistry and Molecular BiologyKyoto Pharmaceutical UniversityKyotoJapan
| | - Youhei Saito
- Department of Biochemistry and Molecular BiologyKyoto Pharmaceutical UniversityKyotoJapan
| | - Yasunori Fukumoto
- Department of Molecular Cell Biology, Graduate School of Pharmaceutical SciencesChiba UniversityChibaJapan
| | - Noritaka Yamaguchi
- Department of Molecular Cell Biology, Graduate School of Pharmaceutical SciencesChiba UniversityChibaJapan
| | - Naoto Yamaguchi
- Department of Molecular Cell Biology, Graduate School of Pharmaceutical SciencesChiba UniversityChibaJapan
| | - Yuji Nakayama
- Department of Biochemistry and Molecular BiologyKyoto Pharmaceutical UniversityKyotoJapan
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18
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Chaudhuri R, Bhattacharya S, Dash J, Bhattacharya S. Recent Update on Targeting c-MYC G-Quadruplexes by Small Molecules for Anticancer Therapeutics. J Med Chem 2020; 64:42-70. [PMID: 33355454 DOI: 10.1021/acs.jmedchem.0c01145] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Guanine-rich DNA sequences have the propensity to adopt four-stranded tetrahelical G-quadruplex (G4) structures that are overrepresented in gene promoters. The structural polymorphism and physicochemical properties of these non-Watson-Crick G4 structures make them important targets for drug development. The guanine-rich nuclease hypersensitivity element III1 present in the upstream of P1 promoter of c-MYC oncogene has the ability to form an intramolecular parallel G4 structure. The G4 structure that forms transiently in the c-MYC promoter functions as a transcriptional repressor element. The c-MYC oncogene is overexpressed in a wide variety of cancers and plays a key role in cancer progression. Till now, a large number of compounds that are capable of interacting and stabilizing thec-MYC G4 have been reported. In this review, we summarize various c-MYC G4 specific molecules and discuss their effects on c-MYC gene expression in vitro and in vivo.
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Affiliation(s)
- Ritapa Chaudhuri
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Semantee Bhattacharya
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Santanu Bhattacharya
- School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.,Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
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19
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Fambrini M, Usai G, Vangelisti A, Mascagni F, Pugliesi C. The plastic genome: The impact of transposable elements on gene functionality and genomic structural variations. Genesis 2020; 58:e23399. [DOI: 10.1002/dvg.23399] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/07/2020] [Accepted: 11/10/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
| | - Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
| | - Alberto Vangelisti
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
| | - Flavia Mascagni
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
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20
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Sun D, Li H, Cao M, He S, Lei L, Peng J, Chen W. Cancer burden in China: trends, risk factors and prevention. Cancer Biol Med 2020; 17:879-895. [PMID: 33299641 PMCID: PMC7721090 DOI: 10.20892/j.issn.2095-3941.2020.0387] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022] Open
Abstract
As the most populous country in the world, China has made strides in health promotion in the past few decades. With the aging population, the burden of cancer in China continues to grow. Changes in risk factors for cancer, especially diet, obesity, diabetes, and air pollution, continue to fuel the shift of cancer transition in China. The burden of upper gastrointestinal cancer in China is decreasing, but still heavy. The rising burden of colorectal, prostate, and breast cancers is also significant. Lung cancer became the top cause of cancer-related deaths, together with smoking as the most important contributor to cancer deaths. The Chinese government has taken several approaches to control cancer and cancer-related risk factors. Many achievements have been made, but some challenges remain. Health China 2030 is ambitious and depicts a bright vision of the future for cancer control in China. The decrease in the cancer burden in China will require cross-sector collaboration and coordinated efforts on primary and secondary preventions by governments, public health organizations, and individuals. In this review, we describe the trends of cancer burden and discuss cancer-related risk factors in China, identifying strategies to reduce the burden of cancer in China.
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Affiliation(s)
- Dianqin Sun
- Department of Cancer Screening, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - He Li
- Department of Cancer Screening, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Maomao Cao
- Department of Cancer Screening, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Siyi He
- Department of Cancer Screening, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Lin Lei
- Department of Cancer Prevention and Control, Shenzhen Center for Chronic Disease Control, Shenzhen 518020, China
| | - Ji Peng
- Department of Cancer Prevention and Control, Shenzhen Center for Chronic Disease Control, Shenzhen 518020, China
| | - Wanqing Chen
- Department of Cancer Screening, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
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21
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Machitani M, Yasukawa M, Nakashima J, Furuichi Y, Masutomi K. RNA-dependent RNA polymerase, RdRP, a promising therapeutic target for cancer and potentially COVID-19. Cancer Sci 2020; 111:3976-3984. [PMID: 32805774 PMCID: PMC7461281 DOI: 10.1111/cas.14618] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 12/12/2022] Open
Abstract
A recent outbreak of coronavirus disease (COVID-19) caused by the novel severe acute respiratory syndrome coronavirus 2 has driven a global pandemic with catastrophic consequences. The rapid development of promising therapeutic strategies against COVID-19 is keenly anticipated. Family Coronaviridae comprises positive, single-stranded RNA viruses that use RNA-dependent RNA polymerase (RdRP) for viral replication and transcription. As the RdRP of viruses in this family and others plays a pivotal role in infection, it is a promising therapeutic target for developing antiviral agents against them. A critical genetic driver for many cancers is the catalytic subunit of telomerase: human telomerase reverse transcriptase (hTERT), identified initially as an RNA-dependent DNA polymerase. However, even though hTERT is a DNA polymerase, it has phylogenetic and structural similarities to viral RdRPs. Researchers worldwide, including the authors of this review, are engaged in developing therapeutic strategies targeting hTERT. We have published a series of papers reporting that hTERT has RdRP activity and that this RdRP activity in hTERT is essential for tumor formation. Here, we review the enzymatic function of RdRP in virus proliferation and tumor development, reminding us of how the study of the novel coronavirus has brought us to the unexpected intersection of cancer research and RNA virus research.
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Affiliation(s)
- Mitsuhiro Machitani
- Division of Cancer Stem CellNational Cancer Center Research InstituteTokyoJapan
| | - Mami Yasukawa
- Division of Cancer Stem CellNational Cancer Center Research InstituteTokyoJapan
| | - Jotaro Nakashima
- Division of Cancer Stem CellNational Cancer Center Research InstituteTokyoJapan
| | | | - Kenkichi Masutomi
- Division of Cancer Stem CellNational Cancer Center Research InstituteTokyoJapan
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22
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Górka M, Żerko S, Konrat R, Koźmiński W, Kurzbach D. 1H, 13C and 15N backbone resonance assignment of BRCA1 fragment 219-504. BIOMOLECULAR NMR ASSIGNMENTS 2020; 14:289-293. [PMID: 32583165 PMCID: PMC7462910 DOI: 10.1007/s12104-020-09963-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
The breast cancer susceptibility protein 1 (BRCA1) plays a central role in the suppression of human breast and ovarian cancer. Germ line mutations of the BRCA1 gene are responsible for the hereditary breast and ovarian cancer (HBOC) syndrome. Here were report 1H, 13C, and 15N resonance assignments for the intrinsically disordered BRCA1 fragment 219-504, which contains important interaction sites for the proto-oncogenic transcription factor MYC as well as for p53. A nuclear magnetic resonance assignment was achieved at 18.8 T magnetic field strength using a 5D HN(CA)CONH experiment and its associated 4D H(NCA)CONH and 4D (H)N(CA)CONH experiments. 13Cα and 13Cβ assignments were obtained using a 5D HabCabCONH experiment. With this strategy, 90% of 1H/15N backbone pairs could be assigned. Similarly, 264 C' resonances were assigned corresponding to 86% of the total number of C' atoms. In addition, 252 Cβ resonances (i.e. 85%) were assigned, together with 461 attached Hβ nuclei, as well as 264 (i.e. 86%) Cα resonances, together with 275 attached Hα nuclei.
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Affiliation(s)
- Michał Górka
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Szymon Żerko
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Robert Konrat
- Department for Structural and Computational Biology, University Vienna, Campus Vienna BioCenter 5, 1030, Vienna, Austria
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Dennis Kurzbach
- Faculty of Chemistry, Institute of Biological Chemistry, University Vienna, Währinger Straße 38, 1090, Vienna, Austria.
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23
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Goto K, Roca Suarez AA, Wrensch F, Baumert TF, Lupberger J. Hepatitis C Virus and Hepatocellular Carcinoma: When the Host Loses Its Grip. Int J Mol Sci 2020; 21:ijms21093057. [PMID: 32357520 PMCID: PMC7246584 DOI: 10.3390/ijms21093057] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 02/06/2023] Open
Abstract
Chronic infection with hepatitis C virus (HCV) is a major cause of hepatocellular carcinoma (HCC). Novel treatments with direct-acting antivirals achieve high rates of sustained virologic response; however, the HCC risk remains elevated in cured patients, especially those with advanced liver disease. Long-term HCV infection causes a persistent and accumulating damage of the liver due to a combination of direct and indirect pro-oncogenic mechanisms. This review describes the processes involved in virus-induced disease progression by viral proteins, derailed signaling, immunity, and persistent epigenetic deregulation, which may be instrumental to develop urgently needed prognostic biomarkers and as targets for novel chemopreventive therapies.
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Affiliation(s)
- Kaku Goto
- Université de Strasbourg, F-67000 Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg (IVH), F-67000 Strasbourg, France
| | - Armando Andres Roca Suarez
- Université de Strasbourg, F-67000 Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg (IVH), F-67000 Strasbourg, France
| | - Florian Wrensch
- Université de Strasbourg, F-67000 Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg (IVH), F-67000 Strasbourg, France
| | - Thomas F. Baumert
- Université de Strasbourg, F-67000 Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg (IVH), F-67000 Strasbourg, France
- Pôle Hépato-digestif, Institut Hopitalo-Universitaire, F-67000 Strasbourg, France
- Institut Universitaire de France, F-75231 Paris, France
- Correspondence: (T.F.B.); (J.L.); Tel.: +33-3-68-85-37-03 (T.F.B. & J.L.); Fax: +33-3-68-85-37-24 (T.F.B. & J.L.)
| | - Joachim Lupberger
- Université de Strasbourg, F-67000 Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg (IVH), F-67000 Strasbourg, France
- Correspondence: (T.F.B.); (J.L.); Tel.: +33-3-68-85-37-03 (T.F.B. & J.L.); Fax: +33-3-68-85-37-24 (T.F.B. & J.L.)
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Abstract
MEK, a central component of the Ras/MAPK cascade, is mutated in human tumors and developmental disorders. Recent studies are beginning to dissect the mechanisms that make these MEK mutants hyperactive.
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Affiliation(s)
- Lee Bardwell
- Department of Developmental and Cell Biology, 2208 Natural Sciences I, University of California, Irvine, CA 92697-2300, USA.
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Ghosh S, Brown AM, Jenkins C, Campbell K. Viral Vector Systems for Gene Therapy: A Comprehensive Literature Review of Progress and Biosafety Challenges. APPLIED BIOSAFETY 2020; 25:7-18. [PMID: 36033383 PMCID: PMC9134621 DOI: 10.1177/1535676019899502] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
INTRODUCTION National Institutes of Health (NIH) defines gene therapy as an experimental technique that uses genes to treat or prevent disease. Although gene therapy is a promising treatment option for a number of diseases (including inherited disorders, some types of cancer, and certain viral infections), the technique remains risky and is still under study to make sure that it will be effective and safe. METHODS Applications of viral vectors and nonviral gene delivery systems have found an encouraging new beginning in gene therapy in recent years. Although several viral vectors and nonviral gene delivery systems have been developed in the past 3 decades, no one delivery system can be applied in gene therapy to all cell types in vitro and in vivo. Furthermore, the use of viral vector systems (both in vitro and in vivo) present unique occupational health and safety challenges. In this review article, we discuss the biosafety challenges and the current framework of risk assessment for working with the viral vector systems. DISCUSSION The recent advances in the field of gene therapy is exciting, but it is important for scientists, institutional biosafety committees, and biosafety officers to safeguard public trust in the use of this technology in clinical trials and make conscious efforts to engage the public through ongoing forums and discussions.
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Affiliation(s)
- Sumit Ghosh
- The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Alex M. Brown
- The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Chris Jenkins
- Clinical Biosafety Services, A Division of Sabai Global, Wildwood, MO, USA
| | - Katie Campbell
- The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
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Kubota S, Ishikawa T, Kawata K, Hattori T, Nishida T. Retrotransposons Manipulating Mammalian Skeletal Development in Chondrocytes. Int J Mol Sci 2020; 21:ijms21051564. [PMID: 32106563 PMCID: PMC7084347 DOI: 10.3390/ijms21051564] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 12/14/2022] Open
Abstract
Retrotransposons are genetic elements that copy and paste themselves in the host genome through transcription, reverse-transcription, and integration processes. Along with their proliferation in the genome, retrotransposons inevitably modify host genes around the integration sites, and occasionally create novel genes. Even now, a number of retrotransposons are still actively editing our genomes. As such, their profound role in the evolution of mammalian genomes is obvious; thus, their contribution to mammalian skeletal evolution and development is also unquestionable. In mammals, most of the skeletal parts are formed and grown through a process entitled endochondral ossification, in which chondrocytes play central roles. In this review, current knowledge on the evolutional, physiological, and pathological roles of retrotransposons in mammalian chondrocyte differentiation and cartilage development is summarized. The possible biological impact of these mobile genetic elements in the future is also discussed.
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27
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Ullrich CI, Aloni R, Saeed MEM, Ullrich W, Efferth T. Comparison between tumors in plants and human beings: Mechanisms of tumor development and therapy with secondary plant metabolites. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2019; 64:153081. [PMID: 31568956 DOI: 10.1016/j.phymed.2019.153081] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 08/30/2019] [Accepted: 09/02/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Human tumors are still a major threat to human health and plant tumors negatively affect agricultural yields. Both areas of research are developing largely independent of each other. Treatment of both plant and human tumors remains unsatisfactory and novel therapy options are urgently needed. HYPOTHESIS The concept of this paper is to compare cellular and molecular mechanisms of tumor development in plants and human beings and to explore possibilities to develop novel treatment strategies based on bioactive secondary plant metabolites. The interdisciplinary discourse may unravel commonalities and differences in the biology of plant and human tumors as basis for rational drug development. RESULTS Plant tumors and galls develop upon infection by bacteria (e.g. Agrobacterium tumefaciens and A. vitis, which harbor oncogenic T-DNA) and by insects (e.g. gall wasps, aphids). Plant tumors are benign, i.e. they usually do not ultimately kill their host, but they can lead to considerable economic damage due to reduced crop yields of cultivated plants. Human tumors develop by biological carcinogenesis (i.e. viruses and other infectious agents), chemical carcinogenesis (anthropogenic and non-anthropogenic environmental toxic xenobiotics) and physical carcinogenesis (radioactivity, UV-radiation). The majority of human tumors are malignant with lethal outcome. Although treatments for both plant and human tumors are available (antibiotics and apathogenic bacterial strains for plant tumors, cytostatic drugs for human tumors), treatment successes are non-satisfactory, because of drug resistance and the severe adverse side effects. In human beings, attacks by microbes are repelled by cellular immunity (i.e. innate and acquired immune systems). Plants instead display chemical defense mechanisms, whereby constitutively expressed phytoanticipin compounds compare to the innate human immune system, the acquired human immune system compares to phytoalexins, which are induced by appropriate biotic or abiotic stressors. Some chemical weapons of this armory of secondary metabolites are also active against plant galls. There is a mutual co-evolution between plant defense and animals/human beings, which was sometimes referred to as animal plant warfare. As a consequence, hepatic phase I-III metabolization and excretion developed in animals and human beings to detoxify harmful phytochemicals. On the other hand, plants invented "pro-drugs" during evolution, which are activated and toxified in animals by this hepatic biotransformation system. Recent efforts focus on phytochemicals that specifically target tumor-related mechanisms and proteins, e.g. angiogenic or metastatic inhibitors, stimulators of the immune system to improve anti-tumor immunity, specific cell death or cancer stem cell inhibitors, inhibitors of DNA damage and epigenomic deregulation, specific inhibitors of driver genes of carcinogenesis (e.g. oncogenes), inhibitors of multidrug resistance (i.e. ABC transporter efflux inhibitors), secondary metabolites against plant tumors. CONCLUSION The exploitation of bioactive secondary metabolites to treat plant or human tumors bears a tremendous therapeutic potential. Although there are fundamental differences between human and plant tumors, either isolated phytochemicals and their (semi)synthetic derivatives or chemically defined and standardized plant extracts may offer new therapy options to decrease human tumor incidence and mortality as well as to increase agricultural yields by fighting crown galls.
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Affiliation(s)
- Cornelia I Ullrich
- Department of Biology, Darmstadt University of Technology, Schnittspahnstr. 3-5, Darmstadt 64287, Germany
| | - Roni Aloni
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Mohamed E M Saeed
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz 55128, Germany
| | - Wolfram Ullrich
- Department of Biology, Darmstadt University of Technology, Schnittspahnstr. 3-5, Darmstadt 64287, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz 55128, Germany.
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Unity and diversity among viral kinases. Gene 2019; 723:144134. [PMID: 31589960 DOI: 10.1016/j.gene.2019.144134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 09/12/2019] [Accepted: 09/16/2019] [Indexed: 12/27/2022]
Abstract
Viral kinases are known to undergo autophosphorylation and also phosphorylate viral and host substrates. Viral kinases have been implicated in various diseases and are also known to acquire host kinases for mimicking cellular functions and exhibit virulence. Although substantial analyses have been reported in the literature on diversity of viral kinases, there is a gap in the understanding of sequence and structural similarity among kinases from different classes of viruses. In this study, we performed a comprehensive analysis of protein kinases encoded in viral genomes. Homology search methods have been used to identify kinases from 104,282 viral genomic datasets. Serine/threonine and tyrosine kinases are identified only in 390 viral genomes. Out of seven viral classes that are based on nature of genetic material, only viruses having double-stranded DNA and single-stranded RNA retroviruses are found to encode kinases. The 716 identified protein kinases are classified into 63 subfamilies based on their sequence similarity within each cluster, and sequence signatures have been identified for each subfamily. 11 clusters are well represented with at least 10 members in each of these clusters. Kinases from dsDNA viruses, Phycodnaviridae which infect green algae and Herpesvirales that infect vertebrates including human, form a major group. From our analysis, it has been observed that the protein kinases in viruses belonging to same taxonomic lineages form discrete clusters and the kinases encoded in alphaherpesvirus form host-specific clusters. A comprehensive sequence and structure-based analysis enabled us to identify the conserved residues or motifs in kinase catalytic domain regions across all viral kinases. Conserved sequence regions that are specific to a particular viral kinase cluster and the kinases that show close similarity to eukaryotic kinases were identified by using sequence and three-dimensional structural regions of eukaryotic kinases as reference. The regions specific to each viral kinase cluster can be used as signatures in the future in classifying uncharacterized viral kinases. We note that kinases from giant viruses Marseilleviridae have close similarity to viral oncogenes in the functional regions and in putative substrate binding regions indicating their possible role in cancer.
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Tamirat MZ, Koivu M, Elenius K, Johnson MS. Structural characterization of EGFR exon 19 deletion mutation using molecular dynamics simulation. PLoS One 2019; 14:e0222814. [PMID: 31536605 PMCID: PMC6752865 DOI: 10.1371/journal.pone.0222814] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/06/2019] [Indexed: 12/18/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) is a tyrosine kinase receptor important in diverse biological processes including cell proliferation and survival. Upregulation of EGFR activity due to over-expression or mutation is widely implicated in cancer. Activating somatic mutations of the EGFR kinase are postulated to affect the conformation and/or stability of the protein, shifting the EGFR inactive-active state equilibrium towards the activated state. Here, we examined a common EGFR deletion mutation, Δ746ELREA750, which is frequently observed in non-small cell lung cancer patients. By using molecular dynamics simulation, we investigated the structural effects of the mutation that lead to the experimentally reported increases in kinase activity. Simulations of the active form wild-type and ΔELREA EGFRs revealed the deletion stabilizes the αC helix of the kinase domain, which is located adjacent to the deletion site, by rigidifying the flexible β3-αC loop that accommodates the ELREA sequence. Consequently, the αC helix is stabilized in the “αC-in” active conformation that would prolong the time of the activated state. Moreover, in the mutant kinase, a salt bridge between E762 and K745, which is key for EGFR activity, was also stabilized during the simulation. Additionally, the interaction between EGFR and ATP was favored by ΔELREA EGFR over wild-type EGFR, as reflected by the number of hydrogen bonds formed and the free energy of binding. Simulation of inactive EGFR suggested the deletion would promote a shift from the inactive conformation towards active EGFR, which is supported by the inward movement of the αC helix. The MDS results also align with the effects of tyrosine kinase inhibitors on ΔELREA and wild-type EGFR lung cancer cell lines, where more pronounced inhibition was observed against ΔELREA than for wild-type EGFR by inhibitors recognizing the active kinase conformation.
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Affiliation(s)
- Mahlet Z. Tamirat
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Marika Koivu
- Medicity Research Laboratories and Institute of Biomedicine, University of Turku, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
| | - Klaus Elenius
- Medicity Research Laboratories and Institute of Biomedicine, University of Turku, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Department of Oncology and Radiotherapy, University of Turku and Turku University Hospital, Turku, Finland
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- * E-mail:
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30
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Minarovits J, Niller HH. Truncated oncoproteins of retroviruses and hepatitis B virus: A lesson in contrasts. INFECTION GENETICS AND EVOLUTION 2019; 73:342-357. [DOI: 10.1016/j.meegid.2019.05.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/14/2019] [Accepted: 05/27/2019] [Indexed: 02/07/2023]
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Abstract
The PI3K/AKT/mTOR pathway is frequently activated in various human cancers and has been considered a promising therapeutic target. Many of the positive regulators of the PI3K/AKT/mTOR axis, including the catalytic (p110α) and regulatory (p85α), of class IA PI3K, AKT, RHEB, mTOR, and eIF4E, possess oncogenic potentials, as demonstrated by transformation assays in vitro and by genetically engineered mouse models in vivo. Genetic evidences also indicate their roles in malignancies induced by activation of the upstream oncoproteins including receptor tyrosine kinases and RAS and those induced by the loss of the negative regulators of the PI3K/AKT/mTOR pathway such as PTEN, TSC1/2, LKB1, and PIPP. Possible mechanisms by which the PI3K/AKT/mTOR axis contributes to oncogenic transformation include stimulation of proliferation, survival, metabolic reprogramming, and invasion/metastasis, as well as suppression of autophagy and senescence. These phenotypic changes are mediated by eIF4E-induced translation of a subset of mRNAs and by other downstream effectors of mTORC1 including S6K, HIF-1α, PGC-1α, SREBP, and ULK1 complex.
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32
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Li W, Yang L, Harris RS, Lin L, Olson TL, Hamele CE, Feith DJ, Loughran TP, Poss M. Retrovirus insertion site analysis of LGL leukemia patient genomes. BMC Med Genomics 2019; 12:88. [PMID: 31208405 PMCID: PMC6580525 DOI: 10.1186/s12920-019-0549-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/06/2019] [Indexed: 02/08/2023] Open
Abstract
Background Large granular lymphocyte (LGL) leukemia is an uncommon cancer characterized by sustained clonal proliferation of LGL cells. Antibodies reactive to retroviruses have been documented in the serum of patients with LGL leukemia. Culture or molecular approaches have to date not been successful in identifying a retrovirus. Methods Because a retrovirus must integrate into the genome of an infected cell, we focused our efforts on detecting a novel retrovirus integration site in the clonally expanded LGL cells. We present a new computational tool that uses long-insert mate pair sequence data to search the genome of LGL leukemia cells for retrovirus integration sites. We also utilize recently published methods to interrogate the status of polymorphic human endogenous retrovirus type K (HERV-K) provirus in patient genomes. Results Our data show that there are no new retrovirus insertions in LGL genomes of LGL leukemia patients. However, our insertion call tool did detect four HERV-K provirus integration sites that are polymorphic in the human population but absent from the human reference genome, hg19. To determine if the prevalence of these or other polymorphic proviral HERV-Ks differed between LGL leukemia patients and the general population, we used a recently developed tool that reports sites in the human genome occupied by a known proviral HERV-K. We report that there are significant differences in the number of polymorphic HERV-Ks in the genomes of LGL leukemia patients of European origin compared to individuals with European ancestry in the 1000 genomes (KGP) data. Conclusions Our study confirms that the clonal expansion of LGL cells in LGL leukemia is not driven by the integration of a new infectious or endogenous retrovirus, although we do not rule out that these cells are responding to retroviral antigens produced in other cell types. However, our computational analyses revealed that the genomes of LGL leukemia patients carry a higher burden of polymorphic HERV-K proviruses compare to individuals from KGP of European ancestry. Our research emphasizes the merits of comprehensive genomic assessment of HERV-K in cancer samples and suggests that further analyses to determine contributions of HERV-K to LGL leukemia are warranted. Electronic supplementary material The online version of this article (10.1186/s12920-019-0549-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Weiling Li
- The School of Electrical Engineering and Computer Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lei Yang
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Robert S Harris
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lin Lin
- Department of Statistics, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Thomas L Olson
- University of Virginia Cancer Center and Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, Virginia, 22908, USA
| | - Cait E Hamele
- University of Virginia Cancer Center and Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, Virginia, 22908, USA
| | - David J Feith
- University of Virginia Cancer Center and Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, Virginia, 22908, USA
| | - Thomas P Loughran
- University of Virginia Cancer Center and Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, Virginia, 22908, USA
| | - Mary Poss
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA. .,University of Virginia Cancer Center and Department of Medicine, Division of Hematology & Oncology, University of Virginia, Charlottesville, Virginia, 22908, USA.
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33
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Broecker F, Moelling K. What viruses tell us about evolution and immunity: beyond Darwin? Ann N Y Acad Sci 2019; 1447:53-68. [PMID: 31032941 PMCID: PMC6850104 DOI: 10.1111/nyas.14097] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/09/2019] [Accepted: 03/20/2019] [Indexed: 12/14/2022]
Abstract
We describe mechanisms of genetic innovation mediated by viruses and related elements that, during evolution, caused major genetic changes beyond what was anticipated by Charles Darwin. Viruses and related elements introduced genetic information and have shaped the genomes and immune systems of all cellular life forms. None of these mechanisms contradict Darwin's theory of evolution but extend it by means of sequence information that has recently become available. Not only do small increments of genetic information contribute to evolution, but also do major events such as infection by viruses or bacteria, which can supply new genetic information to a host by horizontal gene transfer. Thereby, viruses and virus-like elements act as major drivers of evolution.
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Affiliation(s)
- Felix Broecker
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Karin Moelling
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Max Planck Institute for Molecular Genetics, Berlin, Germany
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34
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Chen YF, Xia Y. Convergent perturbation of the human domain-resolved interactome by viruses and mutations inducing similar disease phenotypes. PLoS Comput Biol 2019; 15:e1006762. [PMID: 30759076 PMCID: PMC6373925 DOI: 10.1371/journal.pcbi.1006762] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 01/07/2019] [Indexed: 12/14/2022] Open
Abstract
An important goal of systems medicine is to study disease in the context of genetic and environmental perturbations to the human interactome network. For diseases with both genetic and infectious contributors, a key postulate is that similar perturbations of the human interactome by either disease mutations or pathogens can have similar disease consequences. This postulate has so far only been tested for a few viral species at the level of whole proteins. Here, we expand the scope of viral species examined, and test this postulate more rigorously at the higher resolution of protein domains. Focusing on diseases with both genetic and viral contributors, we found significant convergent perturbation of the human domain-resolved interactome by endogenous genetic mutations and exogenous viral proteins inducing similar disease phenotypes. Pan-cancer, pan-oncovirus analysis further revealed that domains of human oncoproteins either physically targeted or structurally mimicked by oncoviruses are enriched for cancer driver rather than passenger mutations, suggesting convergent targeting of cancer driver pathways by diverse oncoviruses. Our study provides a framework for high-resolution, network-based comparison of various disease factors, both genetic and environmental, in terms of their impacts on the human interactome.
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Affiliation(s)
| | - Yu Xia
- Department of Bioengineering, McGill University, Montreal, Quebec, Canada
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35
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Vogt PK. The Importance of Being Non-Defective: A Mini Review Dedicated to the Memory of Jan Svoboda. Viruses 2019; 11:v11010080. [PMID: 30669277 PMCID: PMC6360021 DOI: 10.3390/v11010080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 01/15/2019] [Accepted: 01/16/2019] [Indexed: 11/18/2022] Open
Abstract
Jan Svoboda triggered investigations on non-defective avian sarcoma viruses. These viruses were a critical factor in the genetic understanding of retroviruses. They provided the single and unique access to the field and facilitated the discovery of the first oncogene src and of the cellular origin of retroviral oncogenes. They continue to be of importance as singularly effective expression vectors that have provided insights into the molecular functions of numerous oncogenes. Combined with the contributions to the validation of the provirus hypothesis, Jan Svoboda’s investigations of non-defective avian sarcoma viruses have shaped a large and important part of retrovirology.
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Affiliation(s)
- Peter K Vogt
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
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36
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Virzì A, Roca Suarez AA, Baumert TF, Lupberger J. Oncogenic Signaling Induced by HCV Infection. Viruses 2018; 10:v10100538. [PMID: 30279347 PMCID: PMC6212953 DOI: 10.3390/v10100538] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 09/29/2018] [Accepted: 09/30/2018] [Indexed: 02/07/2023] Open
Abstract
The liver is frequently exposed to toxins, metabolites, and oxidative stress, which can challenge organ function and genomic stability. Liver regeneration is therefore a highly regulated process involving several sequential signaling events. It is thus not surprising that individual oncogenic mutations in hepatocytes do not necessarily lead to cancer and that the genetic profiles of hepatocellular carcinomas (HCCs) are highly heterogeneous. Long-term infection with hepatitis C virus (HCV) creates an oncogenic environment by a combination of viral protein expression, persistent liver inflammation, oxidative stress, and chronically deregulated signaling events that cumulate as a tipping point for genetic stability. Although novel direct-acting antivirals (DAA)-based treatments efficiently eradicate HCV, the associated HCC risk cannot be fully eliminated by viral cure in patients with advanced liver disease. This suggests that HCV may persistently deregulate signaling pathways beyond viral cure and thereby continue to perturb cancer-relevant gene function. In this review, we summarize the current knowledge about oncogenic signaling pathways derailed by chronic HCV infection. This will not only help to understand the mechanisms of hepatocarcinogenesis but will also highlight potential chemopreventive strategies to help patients with a high-risk profile of developing HCC.
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Affiliation(s)
- Alessia Virzì
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, 67000 Strasbourg, France.
- Université de Strasbourg, 67000 Strasbourg, France.
| | - Armando Andres Roca Suarez
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, 67000 Strasbourg, France.
- Université de Strasbourg, 67000 Strasbourg, France.
| | - Thomas F Baumert
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, 67000 Strasbourg, France.
- Université de Strasbourg, 67000 Strasbourg, France.
- Pôle Hépato-digestif, Institut Hospitalo-universitaire, Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France.
| | - Joachim Lupberger
- Inserm, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, 67000 Strasbourg, France.
- Université de Strasbourg, 67000 Strasbourg, France.
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37
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Ozsvari B, Sotgia F, Lisanti MP. A new mutation-independent approach to cancer therapy: Inhibiting oncogenic RAS and MYC, by targeting mitochondrial biogenesis. Aging (Albany NY) 2018; 9:2098-2116. [PMID: 29080556 PMCID: PMC5680558 DOI: 10.18632/aging.101304] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 10/03/2017] [Indexed: 01/22/2023]
Abstract
Here, we used MCF7 cells as a model system to interrogate how MYC/RAS co-operativity contributes to metabolic flux and stemness in breast cancer cells. We compared the behavior of isogenic MCF7 cell lines transduced with c-Myc or H-Ras (G12V), either individually or in combination. Cancer stem cell (CSC) activity was measured using the mammosphere assay. c-Myc augmented both mammosphere formation and mitochondrial respiration, without any effects on glycolytic flux. In contrast, H-Ras (G12V) synergistically augmented both mammosphere formation and glycolysis, but only in combination with c-Myc, directly demonstrating MYC/RAS co-operativity. As c-Myc is known to exert its effects, in part, by stimulating mitochondrial biogenesis, we next examined the effects of another stimulus known to affect mitochondrial biogenesis, i.e. ROS production. To pharmacologically induce oxidative stress, we used Rotenone (a mitochondrial inhibitor) to target mitochondrial complex I. Treatment with Rotenone showed bi-phasic effects; low-dose Rotenone (1 to 2.5 nM) elevated mammosphere formation, while higher doses (10 to 100 nM) were inhibitory. Importantly, the stimulatory effects of Rotenone on CSC propagation were blocked using a mitochondrial-specific anti-oxidant, namely Mito-tempo. Thus, "mild" mitochondrial oxidative stress, originating at Complex I, was sufficient to pheno-copy the effects of c-Myc, effectively promoting CSC propagation. To validate the idea that mitochondrial biogenesis is required to stimulate CSC propagation, we employed Doxycycline, a well-established inhibitor of mitochondrial protein translation. Treatment with Doxycycline was indeed sufficient to block the stimulatory effects of H-Ras (G12V), c-Myc, and Rotenone on CSC propagation. As such, Doxycycline provides a strong rationale for designing new therapeutics to target mitochondrial biogenesis, suggesting a new "mutation-independent" approach to cancer therapy. In support of this notion, most currently successful anti-cancer agents therapeutically target "cell phenotypes", such as increased cell proliferation, rather than specific genetic mutations. Remarkably, we demonstrated that Doxycycline inhibits the effects of diverse oncogenic stimuli, of both i) genetic (MYC/RAS) and ii) environmental (Rotenone) origins. Finally, we discuss the advantages of our "Proteomics-to-Genomics (PTG)" approach for in silico validation of new biomarkers and novel drug targets. In this context, we developed a new Myc-based Mito-Signature consisting of 3 mitochondrial genes (HSPD1; COX5B; TIMM44) for effectively predicting tumor recurrence (HR=4.69; p=2.4e-08) and distant metastasis (HR=4.94; p=2.8e-07), in ER(+) in breast cancer patients. This gene signature could serve as a new companion diagnostic for the early prediction of treatment failure in patients receiving hormonal therapy.
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Affiliation(s)
- Bela Ozsvari
- Translational Medicine, School of Environment and Life Sciences, Biomedical Research Centre (BRC), University of Salford, Greater Manchester, UK.,The Paterson Institute, University of Manchester, Withington, UK
| | - Federica Sotgia
- Translational Medicine, School of Environment and Life Sciences, Biomedical Research Centre (BRC), University of Salford, Greater Manchester, UK.,The Paterson Institute, University of Manchester, Withington, UK
| | - Michael P Lisanti
- Translational Medicine, School of Environment and Life Sciences, Biomedical Research Centre (BRC), University of Salford, Greater Manchester, UK.,The Paterson Institute, University of Manchester, Withington, UK
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38
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Rumlová M, Ruml T. In vitro methods for testing antiviral drugs. Biotechnol Adv 2018; 36:557-576. [PMID: 29292156 PMCID: PMC7127693 DOI: 10.1016/j.biotechadv.2017.12.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/22/2017] [Accepted: 12/27/2017] [Indexed: 12/24/2022]
Abstract
Despite successful vaccination programs and effective treatments for some viral infections, humans are still losing the battle with viruses. Persisting human pandemics, emerging and re-emerging viruses, and evolution of drug-resistant strains impose continuous search for new antiviral drugs. A combination of detailed information about the molecular organization of viruses and progress in molecular biology and computer technologies has enabled rational antivirals design. Initial step in establishing efficacy of new antivirals is based on simple methods assessing inhibition of the intended target. We provide here an overview of biochemical and cell-based assays evaluating the activity of inhibitors of clinically important viruses.
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Affiliation(s)
- Michaela Rumlová
- Department of Biotechnology, University of Chemistry and Technology, Prague 166 28, Czech Republic.
| | - Tomáš Ruml
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague 166 28, Czech Republic.
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39
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Raffeiner P, Schraffl A, Schwarz T, Röck R, Ledolter K, Hartl M, Konrat R, Stefan E, Bister K. Calcium-dependent binding of Myc to calmodulin. Oncotarget 2018; 8:3327-3343. [PMID: 27926480 PMCID: PMC5356885 DOI: 10.18632/oncotarget.13759] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/21/2016] [Indexed: 12/13/2022] Open
Abstract
The bHLH-LZ (basic region/helix-loop-helix/leucine zipper) oncoprotein Myc and the bHLH-LZ protein Max form a binary transcription factor complex controlling fundamental cellular processes. Deregulated Myc expression leads to neoplastic transformation and is a hallmark of most human cancers. The dynamics of Myc transcription factor activity are post-translationally coordinated by defined protein-protein interactions. Here, we present evidence for a second messenger controlled physical interaction between the Ca2+ sensor calmodulin (CaM) and all Myc variants (v-Myc, c-Myc, N-Myc, and L-Myc). The predominantly cytoplasmic Myc:CaM interaction is Ca2+-dependent, and the binding site maps to the conserved bHLH domain of Myc. Ca2+-loaded CaM binds the monomeric and intrinsically disordered Myc protein with high affinity, whereas Myc:Max heterodimers show less, and Max homodimers no affinity for CaM. NMR spectroscopic analyses using alternating mixtures of 15N-labeled and unlabeled preparations of CaM and a monomeric Myc fragment containing the bHLH-LZ domain corroborate the biochemical results on the Myc:CaM interaction and confirm the interaction site mapping. In electrophoretic mobility shift assays, addition of CaM does not affect high-affinity DNA-binding of Myc:Max heterodimers. However, cell-based reporter analyses and cell transformation assays suggest that increasing CaM levels enhance Myc transcriptional and oncogenic activities. Our results point to a possible involvement of Ca2+ sensing CaM in the fine-tuning of Myc function.
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Affiliation(s)
- Philipp Raffeiner
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, A-6020 Innsbruck, Austria.,Present address: Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrea Schraffl
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Thomas Schwarz
- Max F. Perutz Laboratories, Department of Structural and Computational Biology, University of Vienna, A-1030 Vienna, Austria
| | - Ruth Röck
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Karin Ledolter
- Max F. Perutz Laboratories, Department of Structural and Computational Biology, University of Vienna, A-1030 Vienna, Austria
| | - Markus Hartl
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Robert Konrat
- Max F. Perutz Laboratories, Department of Structural and Computational Biology, University of Vienna, A-1030 Vienna, Austria
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Klaus Bister
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, A-6020 Innsbruck, Austria
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40
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Tsuchida N, Murugan AK, Grieco M. Kirsten Ras* oncogene: significance of its discovery in human cancer research. Oncotarget 2018; 7:46717-46733. [PMID: 27102293 PMCID: PMC5216832 DOI: 10.18632/oncotarget.8773] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 04/10/2016] [Indexed: 12/24/2022] Open
Abstract
The KRAS/ K-RAS oncogene is crucially involved in human cancer. The term "oncogene" -- i.e., a gene able to transform a normal cell into a tumor cell - was introduced in 1969, but the word was not used in the human carcinogenesis literature until much later. Transforming Kras and Hras oncogenes from the Kirsten and Harvey sarcoma viruses were not identified until the early 1980s due to the complicated structures of the viral genomes. Orthologs of these viral oncogenes were then found in transforming DNA fragments in human cancers in the form of mutated versions of the HRAS and KRAS proto-oncogenes. Thus, RAS genes were the first human oncogenes to be identified. Subsequent studies showed that mutated KRAS acted as an in vivo oncogenic driver, as indicated by studies of anti-EGFR therapy for metastatic colorectal cancers. This review addresses the historical background and experimental studies that led to the discovery of Kirsten Ras as an oncogene, the role of mutated KRAS in human carcinogenesis, and recent therapeutic studies of cancer cells with KRAS mutations.
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Affiliation(s)
- Nobuo Tsuchida
- Graduate School of Medical and Dental Sciences, Tokyo Medical Dental University, Yushima, Bunkyo-ku, Tokyo, Japan
| | | | - Michele Grieco
- DiSTABiF, Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università di Napoli, Caserta, Italy
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41
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Honda T, Morii M, Nakayama Y, Suzuki K, Yamaguchi N, Yamaguchi N. v-Src-driven transformation is due to chromosome abnormalities but not Src-mediated growth signaling. Sci Rep 2018; 8:1063. [PMID: 29348492 PMCID: PMC5773541 DOI: 10.1038/s41598-018-19599-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/04/2018] [Indexed: 12/03/2022] Open
Abstract
v-Src is the first identified oncogene product and has a strong tyrosine kinase activity. Much of the literature indicates that v-Src expression induces anchorage-independent and infinite cell proliferation through continuous stimulation of growth signaling by v-Src activity. Although all of v-Src-expressing cells are supposed to form transformed colonies, low frequencies of v-Src-induced colony formation have been observed so far. Using cells that exhibit high expression efficiencies of inducible v-Src, we show that v-Src expression causes cell-cycle arrest through p21 up-regulation despite ERK activation. v-Src expression also induces chromosome abnormalities and unexpected suppression of v-Src expression, leading to p21 down-regulation and ERK inactivation. Importantly, among v-Src-suppressed cells, only a limited number of cells gain the ability to re-proliferate and form transformed colonies. Our findings provide the first evidence that v-Src-driven transformation is attributed to chromosome abnormalities, but not continuous stimulation of growth signaling, possibly through stochastic genetic alterations.
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Affiliation(s)
- Takuya Honda
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
| | - Mariko Morii
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
| | - Yuji Nakayama
- Department of Biochemistry and Molecular Biology, Kyoto Pharmaceutical University, Kyoto, 607-8414, Japan
| | - Ko Suzuki
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
| | - Noritaka Yamaguchi
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
| | - Naoto Yamaguchi
- Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan.
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42
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Production of Anti-c-Myc Monoclonal Antibody Inhibiting DNA Binding of c-Myc and Max Dimer by Epitope Peptide–CpG-DNA–Liposome Complex Without Carriers. Int J Pept Res Ther 2017. [DOI: 10.1007/s10989-017-9649-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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43
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Lai YH, Lin SY, Wu YS, Chen HW, Chen JJW. AC-93253 iodide, a novel Src inhibitor, suppresses NSCLC progression by modulating multiple Src-related signaling pathways. J Hematol Oncol 2017; 10:172. [PMID: 29132432 PMCID: PMC5683468 DOI: 10.1186/s13045-017-0539-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 10/30/2017] [Indexed: 02/08/2023] Open
Abstract
Background The tyrosine kinase Src is involved in the progression of many cancers. Moreover, inhibiting Src activity has been shown to obstruct several signaling pathways regulated by the EGFR. Thus, Src is a valuable target molecule in drug development. The purpose of this study was to identify compounds that directly or indirectly modulate Src to suppress lung cancer cell growth and motility and to investigate the molecular mechanisms underlying the effects of these compounds. Methods Human non-small cell lung cancer (NSCLC) cell lines (PC9, PC9/gef, A549, and H1975) with different EGFR statuses were tested by cytotoxicity and proliferation assays after AC-93253 iodide treatment. Src and Src-related protein expression in AC-93253 iodide-treated PC9, PC9/gef, and A549 cells were assessed by western blotting. The effects of AC-93253 iodide on cancer cell colony formation, invasion, and migration were assessed in PC9 and PC9/gef cells. The synergistic effects of gefitinib and AC-93253 iodide were evaluated by combination index (CI)-isobologram analysis in gefitinib-resistant cell lines. The efficacy of AC-93253 iodide in vivo was determined using nude mice treated with either the compound or the vehicle. Results Among the compounds, AC-93253 iodide exhibited the most potent dose-independent inhibitory effects on the activity of Src as well as on that of the Src-related proteins EGFR, STAT3, and FAK. Furthermore, AC-93253 iodide significantly suppressed cancer cell proliferation, colony formation, invasion, and migration in vitro and tumor growth in vivo. AC-93253 iodide sensitized tumor cells to gefitinib treatment regardless of whether the cells were gefitinib-sensitive (PC9) or resistant (H1975 and PC9/gef), indicating that it may exert synergistic effects when used in combination with established therapeutic agents. Our findings also suggested that the inhibitory effects of AC-93253 iodide on lung cancer progression may be attributable to its ability to modulate multiple proteins, including Src, PI3K, JNK, Paxillin, p130cas, MEK, ERK, and EGFR. Conclusions Our data suggest that AC-93253 iodide inhibits NSCLC cell growth and motility by regulating multiple Src-related pathways. Our findings may facilitate the development of therapeutic strategies and anti-tumor drugs that may be useful for treating lung cancer in the future. Electronic supplementary material The online version of this article (10.1186/s13045-017-0539-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yi-Hua Lai
- Institute of Biomedical Sciences, National Chung Hsing University, No. 145, Xingda Rd., South Dist, Taichung, 40227, Taiwan, Republic of China
| | - Sih-Yin Lin
- Institute of Biomedical Sciences, National Chung Hsing University, No. 145, Xingda Rd., South Dist, Taichung, 40227, Taiwan, Republic of China
| | - Yu-Shan Wu
- Department of Chemistry, Tunghai University, Taichung, Taiwan
| | - Huei-Wen Chen
- Graduate Institute of Toxicology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Jeremy J W Chen
- Institute of Biomedical Sciences, National Chung Hsing University, No. 145, Xingda Rd., South Dist, Taichung, 40227, Taiwan, Republic of China. .,Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan. .,Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan. .,Department of Biotechnology, Asia University, Taichung, 41354, Taiwan.
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44
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Chang Y, Moore PS, Weiss RA. Human oncogenic viruses: nature and discovery. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160264. [PMID: 28893931 PMCID: PMC5597731 DOI: 10.1098/rstb.2016.0264] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2017] [Indexed: 12/13/2022] Open
Abstract
Seven kinds of virus collectively comprise an important cause of cancer, particularly in less developed countries and for people with damaged immune systems. Discovered over the past 54 years, most of these viruses are common infections of humankind for which malignancy is a rare consequence. Various cofactors affect the complex interaction between virus and host and the likelihood of cancer emerging. Although individual human tumour viruses exert their malignant effects in different ways, there are common features that illuminate mechanisms of oncogenesis more generally, whether or not there is a viral aetiology.This article is part of the themed issue 'Human oncogenic viruses'.
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Affiliation(s)
- Yuan Chang
- University of Pittsburgh Cancer Institute, 5117 Centre Ave, Res Pav 1.8, Pittsburgh, PA 15213, USA
| | - Patrick S Moore
- University of Pittsburgh Cancer Institute, 5117 Centre Ave, Res Pav 1.8, Pittsburgh, PA 15213, USA
| | - Robin A Weiss
- Division of Infection and Immunity, University College London, Cruciform Bldg 1.3, Gower Street, London WC1 6BT, UK
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45
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Identifying tumor promoting genomic alterations in tumor-associated fibroblasts via retrovirus-insertional mutagenesis. Oncotarget 2017; 8:97231-97245. [PMID: 29228606 PMCID: PMC5722558 DOI: 10.18632/oncotarget.21881] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 09/21/2017] [Indexed: 01/01/2023] Open
Abstract
Tumor-associated fibroblasts (TAFs) are often essential for solid tumor growth. However, few genetic or epigenetic alterations have been found in TAFs during the progression of solid tumors. Employing a tumor-stromal cell co-injection model, we adapted here retroviral-insertional mutagenesis to stromal cells to identify novel tumor-associated genes in TAFs. We successfully identified 20 gene candidates that might modulate tumor growth if altered in TAFs at genomic level. To validate our finding, the function of one of the candidate genes, tubulin tyrosine ligase (Ttl), was further studied in TAFs from fibrosarcoma, colon, breast and hepatocarcinoma. We demonstrated that down-regulated TTL expression in TAFs indeed promoted tumor growth in mice. Interestingly, decreased expression of TTL in tumor stromal cells also correlated with poor outcome in human colon carcinoma. Thus, the co-injection model of tumor cells with retrovirus-modified fibroblasts proved a valid method to identify tumor-modulating genes in TAFs, allowing for a deeper insight into the role of the stroma for tumor development.
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46
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Stefan E, Troppmair J, Bister K. Targeting the Architecture of Deregulated Protein Complexes in Cancer. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 111:101-132. [PMID: 29459029 DOI: 10.1016/bs.apcsb.2017.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The architectures of central signaling hubs are precisely organized by static and dynamic protein-protein interactions (PPIs). Upon deregulation, these PPI platforms are capable to propagate or initiate pathophysiological signaling events. This causes the acquisition of molecular features contributing to the etiology or progression of many diseases, including cancer, where deregulated molecular interactions of signaling proteins have been best studied. The reasons for PPI-dependent reprogramming of cancer-initiating cells are manifold; in many cases, mutations perturb PPIs, enzyme activities, protein abundance, or protein localization. Consequently, the pharmaceutical targeting of PPIs promises to be of remarkable therapeutic value. For this review we have selected three key players of oncogenic signaling which are differently affected by PPI deregulation: two (the small G proteins of the RAS family and the transcription factor MYC) are considered "undruggable" using classical drug discovery approaches and in the case of the third protein discussed here, PKA, standard kinase inhibitors, may be unsuitable in the clinic. These circumstances require alternative strategies, which may lie in pharmaceutical drug interference of critical PPIs accountable for oncogenic signaling.
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Affiliation(s)
- Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria.
| | - Jakob Troppmair
- Daniel Swarovski Research Laboratory, Medical University of Innsbruck, Innsbruck, Austria
| | - Klaus Bister
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
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47
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Viruses as vectors of horizontal transfer of genetic material in eukaryotes. Curr Opin Virol 2017; 25:16-22. [DOI: 10.1016/j.coviro.2017.06.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 05/18/2017] [Accepted: 06/13/2017] [Indexed: 01/04/2023]
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48
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Fajer M, Meng Y, Roux B. The Activation of c-Src Tyrosine Kinase: Conformational Transition Pathway and Free Energy Landscape. J Phys Chem B 2017; 121:3352-3363. [PMID: 27715044 PMCID: PMC5398919 DOI: 10.1021/acs.jpcb.6b08409] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Tyrosine kinases are important cellular signaling allosteric enzymes that regulate cell growth, proliferation, metabolism, differentiation, and migration. Their activity must be tightly controlled, and malfunction can lead to a variety of diseases, particularly cancer. The nonreceptor tyrosine kinase c-Src, a prototypical model system and a representative member of the Src-family, functions as complex multidomain allosteric molecular switches comprising SH2 and SH3 domains modulating the activity of the catalytic domain. The broad picture of self-inhibition of c-Src via the SH2 and SH3 regulatory domains is well characterized from a structural point of view, but a detailed molecular mechanism understanding is nonetheless still lacking. Here, we use advanced computational methods based on all-atom molecular dynamics simulations with explicit solvent to advance our understanding of kinase activation. To elucidate the mechanism of regulation and self-inhibition, we have computed the pathway and the free energy landscapes for the "inactive-to-active" conformational transition of c-Src for different configurations of the SH2 and SH3 domains. Using the isolated c-Src catalytic domain as a baseline for comparison, it is observed that the SH2 and SH3 domains, depending upon their bound orientation, promote either the inactive or active state of the catalytic domain. The regulatory structural information from the SH2-SH3 tandem is allosterically transmitted via the N-terminal linker of the catalytic domain. Analysis of the conformational transition pathways also illustrates the importance of the conserved tryptophan 260 in activating c-Src, and reveals a series of concerted events during the activation process.
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Affiliation(s)
| | | | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637, USA
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49
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Hsp90 dependence of a kinase is determined by its conformational landscape. Sci Rep 2017; 7:43996. [PMID: 28290541 PMCID: PMC5349555 DOI: 10.1038/srep43996] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 02/03/2017] [Indexed: 01/05/2023] Open
Abstract
Heat shock protein 90 (Hsp90) is an abundant molecular chaperone, involved in the folding and activation of 60% of the human kinome. The oncogenic tyrosine kinase v-Src is one of the most stringent client proteins of Hsp90, whereas its almost identical homolog c-Src is only weakly affected by the chaperone. Here, we perform atomistic molecular simulations and in vitro kinase assays to explore the mechanistic differences in the activation of v-Src and c-Src. While activation in c-Src is strictly controlled by ATP-binding and phosphorylation, we find that activating conformational transitions are spontaneously sampled in Hsp90-dependent Src mutants. Phosphorylation results in an enrichment of the active conformation and in an increased affinity for Hsp90. Thus, the conformational landscape of the mutated kinase is reshaped by a broken “control switch”, resulting in perturbations of long-range electrostatics, higher activity and increased Hsp90-dependence.
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50
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Vance RE, Eichberg MJ, Portnoy DA, Raulet DH. Listening to each other: Infectious disease and cancer immunology. Sci Immunol 2017; 2:eaai9339. [PMID: 28783669 PMCID: PMC5927821 DOI: 10.1126/sciimmunol.aai9339] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/21/2016] [Indexed: 12/21/2022]
Abstract
The immune system provides defense against tumors and pathogens. Here, we propose that by elucidating the shared principles of immunity that underlie cancer and infectious disease, oncologists and microbiologists can learn from each other and achieve the deeper mechanistic understanding critical the development of therapeutic approaches.
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Affiliation(s)
- Russell E Vance
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
- Cancer Research Laboratory, University of California, Berkeley, Berkeley, CA 94720, USA
- Immunotherapeutics and Vaccine Research Initiative, University of California, Berkeley, Berkeley, CA 94720, USA
- Center for Emerging and Neglected Disease, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael J Eichberg
- Immunotherapeutics and Vaccine Research Initiative, University of California, Berkeley, Berkeley, CA 94720, USA
- Center for Emerging and Neglected Disease, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Daniel A Portnoy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Cancer Research Laboratory, University of California, Berkeley, Berkeley, CA 94720, USA
- Immunotherapeutics and Vaccine Research Initiative, University of California, Berkeley, Berkeley, CA 94720, USA
- Center for Emerging and Neglected Disease, University of California, Berkeley, Berkeley, CA 94720, USA
- School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - David H Raulet
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Cancer Research Laboratory, University of California, Berkeley, Berkeley, CA 94720, USA
- Immunotherapeutics and Vaccine Research Initiative, University of California, Berkeley, Berkeley, CA 94720, USA
- Center for Emerging and Neglected Disease, University of California, Berkeley, Berkeley, CA 94720, USA
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