1
|
New opportunities and challenges of venom-based and bacteria-derived molecules for anticancer targeted therapy. Semin Cancer Biol 2020; 80:356-369. [PMID: 32846203 DOI: 10.1016/j.semcancer.2020.08.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 08/14/2020] [Accepted: 08/15/2020] [Indexed: 12/24/2022]
Abstract
Due to advances in detection and treatment of cancer, especially the rise in the targeted therapy, the five-year relative survival rate of all cancers has increased significantly. However, according to the analysis of the survival rate of cancer patients in 2019, the survival rate of most cancers is still less than five years. Therefore, to combat complex cancer and further improve the 5-year survival rate of cancer patients, it is necessary to develop some new anticancer drugs. Because of the adaptive evolution of toxic species for millions of years, the venom sac is a "treasure bank", which has millions of biomolecules with high affinity and stability awaiting further development. Complete utilization of venom-based and bacteria-derived drugs in the market is still staggering because of incomplete understanding regarding their mode of action. In this review, we focused on the currently identified targets for anticancer effects based on venomous and bacterial biomolecules, such as ion channels, membrane non-receptor molecules, integrins, and other related target molecules. This review will serve as the key for exploring the molecular mechanisms behind the anticancer potential of venom-based and bacteria-derived drugs and will also lay the path for the development of anticancer targeted therapy.
Collapse
|
2
|
Modahl CM, Brahma RK, Koh CY, Shioi N, Kini RM. Omics Technologies for Profiling Toxin Diversity and Evolution in Snake Venom: Impacts on the Discovery of Therapeutic and Diagnostic Agents. Annu Rev Anim Biosci 2019; 8:91-116. [PMID: 31702940 DOI: 10.1146/annurev-animal-021419-083626] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Snake venoms are primarily composed of proteins and peptides, and these toxins have developed high selectivity to their biological targets. This makes venoms interesting for exploration into protein evolution and structure-function relationships. A single venom protein superfamily can exhibit a variety of pharmacological effects; these variations in activity originate from differences in functional sites, domains, posttranslational modifications, and the formations of toxin complexes. In this review, we discuss examples of how the major venom protein superfamilies have diversified, as well as how newer technologies in the omics fields, such as genomics, transcriptomics, and proteomics, can be used to characterize both known and unknown toxins.Because toxins are bioactive molecules with a rich diversity of activities, they can be useful as therapeutic and diagnostic agents, and successful examples of toxin applications in these areas are also reviewed. With the current rapid pace of technology, snake venom research and its applications will only continue to expand.
Collapse
Affiliation(s)
- Cassandra M Modahl
- Protein Science Lab, Department of Biological Sciences, University of Singapore, Singapore 119077; , ,
| | - Rajeev Kungur Brahma
- Protein Science Lab, Department of Biological Sciences, University of Singapore, Singapore 119077; , ,
| | - Cho Yeow Koh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077;
| | - Narumi Shioi
- Protein Science Lab, Department of Biological Sciences, University of Singapore, Singapore 119077; , , .,Department of Chemistry, Faculty of Science, Fukuoka University, Fukuoka 814-0180, Japan;
| | - R Manjunatha Kini
- Protein Science Lab, Department of Biological Sciences, University of Singapore, Singapore 119077; , ,
| |
Collapse
|
3
|
Wiezel GA, Shibao PYT, Cologna CT, Morandi Filho R, Ueira-Vieira C, De Pauw E, Quinton L, Arantes EC. In-Depth Venome of the Brazilian Rattlesnake Crotalus durissus terrificus: An Integrative Approach Combining Its Venom Gland Transcriptome and Venom Proteome. J Proteome Res 2018; 17:3941-3958. [PMID: 30270628 DOI: 10.1021/acs.jproteome.8b00610] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Snake venoms are complex mixtures mainly composed of proteins and small peptides. Crotoxin is one of the most studied components from Crotalus venoms, but many other components are less known due to their low abundance. The venome of Crotalus durissus terrificus, the most lethal Brazilian snake, was investigated by combining its venom gland transcriptome and proteome to create a holistic database of venom compounds unraveling novel toxins. We constructed a cDNA library from C. d. terrificus venom gland using the Illumina platform and investigated its venom proteome through high resolution liquid chromotography-tandem mass spectrometry. After integrating data from both data sets, more than 30 venom components classes were identified by the transcriptomic analysis and 15 of them were detected in the venom proteome. However, few of them (PLA2, SVMP, SVSP, and VEGF) were relatively abundant. Furthermore, only seven expressed transcripts contributed to ∼82% and ∼73% of the abundance in the transcriptome and proteome, respectively. Additionally, novel venom proteins are reported, and we highlight the importance of using different databases to perform the data integration and discuss the structure of the venom components-related transcripts identified. Concluding, this research paves the way for novel investigations and discovery of future pharmacological agents or targets in the antivenom therapy.
Collapse
Affiliation(s)
- Gisele A Wiezel
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto , University of São Paulo , Av. do Café, s/n , 14040-903 Ribeirão Preto , Brazil
| | - Priscila Y T Shibao
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto , University of São Paulo , Av. do Café, s/n , 14040-903 Ribeirão Preto , Brazil
| | - Camila T Cologna
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto , University of São Paulo , Av. do Café, s/n , 14040-903 Ribeirão Preto , Brazil
| | - Romualdo Morandi Filho
- Laboratory of Genetics, Biotechnology Institute , Federal University of Uberlândia , Rua Acre, s/n , 38400-902 Uberlândia , Brazil
| | - Carlos Ueira-Vieira
- Laboratory of Genetics, Biotechnology Institute , Federal University of Uberlândia , Rua Acre, s/n , 38400-902 Uberlândia , Brazil
| | - Edwin De Pauw
- Laboratory of Mass Spectrometry, MolSys Research Unit, Department of Chemistry , University of Liège , Bat. B6c , 4000 Liège , Belgium
| | - Loïc Quinton
- Laboratory of Mass Spectrometry, MolSys Research Unit, Department of Chemistry , University of Liège , Bat. B6c , 4000 Liège , Belgium
| | - Eliane C Arantes
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto , University of São Paulo , Av. do Café, s/n , 14040-903 Ribeirão Preto , Brazil
| |
Collapse
|
4
|
Boldrini-França J, Cologna CT, Pucca MB, Bordon KDCF, Amorim FG, Anjolette FAP, Cordeiro FA, Wiezel GA, Cerni FA, Pinheiro-Junior EL, Shibao PYT, Ferreira IG, de Oliveira IS, Cardoso IA, Arantes EC. Minor snake venom proteins: Structure, function and potential applications. Biochim Biophys Acta Gen Subj 2017; 1861:824-838. [DOI: 10.1016/j.bbagen.2016.12.022] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 12/12/2016] [Accepted: 12/20/2016] [Indexed: 12/20/2022]
|
5
|
Xie B, Huang Y, Baumann K, Fry BG, Shi Q. From Marine Venoms to Drugs: Efficiently Supported by a Combination of Transcriptomics and Proteomics. Mar Drugs 2017; 15:md15040103. [PMID: 28358320 PMCID: PMC5408249 DOI: 10.3390/md15040103] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/20/2017] [Accepted: 03/29/2017] [Indexed: 11/16/2022] Open
Abstract
The potential of marine natural products to become new drugs is vast; however, research is still in its infancy. The chemical and biological diversity of marine toxins is immeasurable and as such an extraordinary resource for the discovery of new drugs. With the rapid development of next-generation sequencing (NGS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), it has been much easier and faster to identify more toxins and predict their functions with bioinformatics pipelines, which pave the way for novel drug developments. Here we provide an overview of related bioinformatics pipelines that have been supported by a combination of transcriptomics and proteomics for identification and function prediction of novel marine toxins.
Collapse
Affiliation(s)
- Bing Xie
- Venomics Research Group, BGI-Shenzhen, Shenzhen 518083, China.
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen 518083, China.
| | - Kate Baumann
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia 4072, Australia.
| | - Bryan Grieg Fry
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia 4072, Australia.
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI, Shenzhen 518083, China.
- BGI Shenzhen Academy of Marine Sciences, BGI Fisheries, BGI, Shenzhen 518083, China.
| |
Collapse
|
6
|
Integrating Perspectives on Animal Venom Diversity: An Introduction to the Symposium. Integr Comp Biol 2016; 56:934-937. [DOI: 10.1093/icb/icw112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
|
7
|
Li R, Yu H, Yue Y, Liu S, Xing R, Chen X, Li P. Combined proteomics and transcriptomics identifies sting-related toxins of jellyfish Cyanea nozakii. J Proteomics 2016; 148:57-64. [PMID: 27461980 DOI: 10.1016/j.jprot.2016.07.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/16/2016] [Accepted: 07/22/2016] [Indexed: 01/22/2023]
Abstract
UNLABELLED Jellyfish sting has become a worldwide issue of critical concern to human health and safety in coastal areas in recent decades. Cyanea nozakii is one of the dominant blooming species and dangerous stingers in China. However, it remains unclear how many and what types of toxins are present in the venom. So, we used a combined transcriptomics and proteomics approach to investigate the venom composition of jellyfish C. nozakii. In total 4,608,524 Illumina valid reads were obtained to de novo assemble to 40,434 unigenes in the transcriptomics analysis. And, a total of 311,635 MS/MS spectra with 12,247 unique MS/MS spectra were generated to 1556 homologous proteins in the proteomics analysis. 174 potential toxin proteins were identified, with 27 proteins homology to the toxins from venomous animals, including phospholipase A2, zinc metalloproteinase-disintegrin agkistin, serine protease inhibitor, plancitoxin-1, alpha-latrocrustotoxin-Lt1a, etc. This study described the transcriptomics and venom proteomics of jellyfish C. nozakii for the first time. Our findings provide a comprehensive understanding of the venom composition of C. nozakii. Furthermore, the results may also be very helpful for the discovery of novel bioactive proteins, as well as the development of effective treatments for jellyfish sting in the future. BIOLOGICAL SIGNIFICANCE Jellyfish Cyanea nozakii is one of the most dangerous stingers in the coast of china. Hundreds of thousands of people would be stung every year and victims suffered a severe pain, itch, swelling, inflammation, wheal and even more serious consequence. However, it remains unclear how many and what types of toxins are present as well as the relationship between the clinical symptoms and toxins. Our combined transcriptomics and proteomics findings can provide a comprehensive understanding of the venom composition of C. nozakii and will also be helpful for the development of effective treatments for jellyfish sting in the future.
Collapse
Affiliation(s)
- Rongfeng Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | - Huahua Yu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | - Yang Yue
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; University of the Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100039, China
| | - Song Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | - Ronge Xing
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | - Xiaolin Chen
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | - Pengcheng Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China.
| |
Collapse
|
8
|
Abstract
Over the last three decades, transcriptomic studies of venom gland cells have continuously evolved, opening up new possibilities for exploring the molecular diversity of animal venoms, a prerequisite for the discovery of new drug candidates and molecular phylogenetics. The molecular complexity of animal venoms is much greater than initially thought. In this review, we describe the different technologies available for transcriptomic studies of venom, from the original individual cloning approaches to the more recent global Next Generation Sequencing strategies. Our understanding of animal venoms is evolving, with the discovery of complex and diverse bio-optimized cocktails of compounds, including mostly peptides and proteins, which are now beginning to be studied by academic and industrial researchers.
Collapse
|
9
|
Bioinformatics-Aided Venomics. Toxins (Basel) 2015; 7:2159-87. [PMID: 26110505 PMCID: PMC4488696 DOI: 10.3390/toxins7062159] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/03/2015] [Accepted: 06/05/2015] [Indexed: 12/12/2022] Open
Abstract
Venomics is a modern approach that combines transcriptomics and proteomics to explore the toxin content of venoms. This review will give an overview of computational approaches that have been created to classify and consolidate venomics data, as well as algorithms that have helped discovery and analysis of toxin nucleic acid and protein sequences, toxin three-dimensional structures and toxin functions. Bioinformatics is used to tackle specific challenges associated with the identification and annotations of toxins. Recognizing toxin transcript sequences among second generation sequencing data cannot rely only on basic sequence similarity because toxins are highly divergent. Mass spectrometry sequencing of mature toxins is challenging because toxins can display a large number of post-translational modifications. Identifying the mature toxin region in toxin precursor sequences requires the prediction of the cleavage sites of proprotein convertases, most of which are unknown or not well characterized. Tracing the evolutionary relationships between toxins should consider specific mechanisms of rapid evolution as well as interactions between predatory animals and prey. Rapidly determining the activity of toxins is the main bottleneck in venomics discovery, but some recent bioinformatics and molecular modeling approaches give hope that accurate predictions of toxin specificity could be made in the near future.
Collapse
|
10
|
Durban J, Pérez A, Sanz L, Gómez A, Bonilla F, Rodríguez S, Chacón D, Sasa M, Angulo Y, Gutiérrez JM, Calvete JJ. Integrated "omics" profiling indicates that miRNAs are modulators of the ontogenetic venom composition shift in the Central American rattlesnake, Crotalus simus simus. BMC Genomics 2013; 14:234. [PMID: 23575160 PMCID: PMC3660174 DOI: 10.1186/1471-2164-14-234] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 03/14/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Understanding the processes that drive the evolution of snake venom is a topic of great research interest in molecular and evolutionary toxinology. Recent studies suggest that ontogenetic changes in venom composition are genetically controlled rather than environmentally induced. However, the molecular mechanisms underlying these changes remain elusive. Here we have explored the basis and level of regulation of the ontogenetic shift in the venom composition of the Central American rattlesnake, Crotalus s. simus using a combined proteomics and transcriptomics approach. RESULTS Proteomic analysis showed that the ontogenetic shift in the venom composition of C. s. simus is essentially characterized by a gradual reduction in the expression of serine proteinases and PLA2 molecules, particularly crotoxin, a β-neurotoxic heterodimeric PLA2, concominantly with an increment of PI and PIII metalloproteinases at age 9-18 months. Comparison of the transcriptional activity of the venom glands of neonate and adult C. s. simus specimens indicated that their transcriptomes exhibit indistinguisable toxin family profiles, suggesting that the elusive mechanism by which shared transcriptomes generate divergent venom phenotypes may operate post-transcriptionally. Specifically, miRNAs with frequency count of 1000 or greater exhibited an uneven distribution between the newborn and adult datasets. Of note, 590 copies of a miRNA targeting crotoxin B-subunit was exclusively found in the transcriptome of the adult snake, whereas 1185 copies of a miRNA complementary to a PIII-SVMP mRNA was uniquely present in the newborn dataset. These results support the view that age-dependent changes in the concentration of miRNA modulating the transition from a crotoxin-rich to a SVMP-rich venom from birth through adulthood can potentially explain what is observed in the proteomic analysis of the ontogenetic changes in the venom composition of C. s. simus. CONCLUSIONS Existing snake venom toxins are the result of early recruitment events in the Toxicofera clade of reptiles by which ordinary genes were duplicated, and the new genes selectively expressed in the venom gland and amplified to multigene families with extensive neofunctionalization throughout the approximately 112-125 million years of ophidian evolution. Our findings support the view that understanding the phenotypic diversity of snake venoms requires a deep knowledge of the mechanisms regulating the transcriptional and translational activity of the venom gland. Our results suggest a functional role for miRNAs. The impact of specific miRNAs in the modulation of venom composition, and the integration of the mechanisms responsible for the generation of these miRNAs in the evolutionary landscape of the snake's venom gland, are further challenges for future research.
Collapse
Affiliation(s)
- Jordi Durban
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Jaime Roig 11, Valencia 46010, Spain
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|