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Alonso LL, van Thiel J, Slagboom J, Dunstan N, Modahl CM, Jackson TNW, Samanipour S, Kool J. Studying Venom Toxin Variation Using Accurate Masses from Liquid Chromatography-Mass Spectrometry Coupled with Bioinformatic Tools. Toxins (Basel) 2024; 16:181. [PMID: 38668606 PMCID: PMC11053424 DOI: 10.3390/toxins16040181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/25/2024] [Accepted: 04/02/2024] [Indexed: 04/29/2024] Open
Abstract
This study provides a new methodology for the rapid analysis of numerous venom samples in an automated fashion. Here, we use LC-MS (Liquid Chromatography-Mass Spectrometry) for venom separation and toxin analysis at the accurate mass level combined with new in-house written bioinformatic scripts to obtain high-throughput results. This analytical methodology was validated using 31 venoms from all members of a monophyletic clade of Australian elapids: brown snakes (Pseudonaja spp.) and taipans (Oxyuranus spp.). In a previous study, we revealed extensive venom variation within this clade, but the data was manually processed and MS peaks were integrated into a time-consuming and labour-intensive approach. By comparing the manual approach to our new automated approach, we now present a faster and more efficient pipeline for analysing venom variation. Pooled venom separations with post-column toxin fractionations were performed for subsequent high-throughput venomics to obtain toxin IDs correlating to accurate masses for all fractionated toxins. This workflow adds another dimension to the field of venom analysis by providing opportunities to rapidly perform in-depth studies on venom variation. Our pipeline opens new possibilities for studying animal venoms as evolutionary model systems and investigating venom variation to aid in the development of better antivenoms.
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Affiliation(s)
- Luis L. Alonso
- Division of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (L.L.A.); (J.S.)
- Centre for Analytical Sciences Amsterdam (CASA), 1012 WX Amsterdam, The Netherlands
| | - Jory van Thiel
- Division of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (L.L.A.); (J.S.)
- Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
- Naturalis Biodiversity Center, 2333 CR Leiden, The Netherlands
| | - Julien Slagboom
- Division of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (L.L.A.); (J.S.)
- Centre for Analytical Sciences Amsterdam (CASA), 1012 WX Amsterdam, The Netherlands
| | | | - Cassandra M. Modahl
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK;
| | - Timothy N. W. Jackson
- Australian Venom Research Unit, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC 3010, Australia;
| | - Saer Samanipour
- Van‘t Hof Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands;
| | - Jeroen Kool
- Division of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; (L.L.A.); (J.S.)
- Centre for Analytical Sciences Amsterdam (CASA), 1012 WX Amsterdam, The Netherlands
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Wachtel E, Bittenbinder MA, van de Velde B, Slagboom J, de Monts de Savasse A, Alonso LL, Casewell NR, Vonk FJ, Kool J. Application of an Extracellular Matrix-Mimicking Fluorescent Polymer for the Detection of Proteolytic Venom Toxins. Toxins (Basel) 2023; 15:toxins15040294. [PMID: 37104232 PMCID: PMC10143632 DOI: 10.3390/toxins15040294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/12/2023] [Accepted: 04/15/2023] [Indexed: 04/28/2023] Open
Abstract
The cytotoxicity caused by snake venoms is a serious medical problem that greatly contributes to the morbidity observed in snakebite patients. The cytotoxic components found in snake venoms belong to a variety of toxin classes and may cause cytotoxic effects by targeting a range of molecular structures, including cellular membranes, the extracellular matrix (ECM) and the cytoskeleton. Here, we present a high-throughput assay (384-well plate) that monitors ECM degradation by snake venom toxins via the application of fluorescent versions of model ECM substrates, specifically gelatin and collagen type I. Both crude venoms and fractionated toxins of a selection of medically relevant viperid and elapid species, separated via size-exclusion chromatography, were studied using the self-quenching, fluorescently labelled ECM-polymer substrates. The viperid venoms showed significantly higher proteolytic degradation when compared to elapid venoms, although the venoms with higher snake venom metalloproteinase content did not necessarily exhibit stronger substrate degradation than those with a lower one. Gelatin was generally more readily cleaved than collagen type I. In the viperid venoms, which were subjected to fractionation by SEC, two (B. jararaca and C. rhodostoma, respectively) or three (E. ocellatus) active proteases were identified. Therefore, the assay allows the study of proteolytic activity towards the ECM in vitro for crude and fractionated venoms.
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Affiliation(s)
- Eric Wachtel
- AIMMS, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Matyas A Bittenbinder
- AIMMS, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1098 XH Amsterdam, The Netherlands
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands
| | - Bas van de Velde
- AIMMS, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1098 XH Amsterdam, The Netherlands
| | - Julien Slagboom
- AIMMS, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1098 XH Amsterdam, The Netherlands
| | - Axel de Monts de Savasse
- AIMMS, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Luis L Alonso
- AIMMS, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1098 XH Amsterdam, The Netherlands
| | - Nicholas R Casewell
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Freek J Vonk
- AIMMS, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1098 XH Amsterdam, The Netherlands
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands
| | - Jeroen Kool
- AIMMS, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1098 XH Amsterdam, The Netherlands
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Alonso LL, Slagboom J, Casewell NR, Samanipour S, Kool J. Metabolome-Based Classification of Snake Venoms by Bioinformatic Tools. Toxins (Basel) 2023; 15:161. [PMID: 36828475 PMCID: PMC9963137 DOI: 10.3390/toxins15020161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/31/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023] Open
Abstract
Snakebite is considered a neglected tropical disease, and it is one of the most intricate ones. The variability found in snake venom is what makes it immensely complex to study. These variations are present both in the big and the small molecules found in snake venom. This study focused on examining the variability found in the venom's small molecules (i.e., mass range of 100-1000 Da) between two main families of venomous snakes-Elapidae and Viperidae-managing to create a model able to classify unknown samples by means of specific features, which can be extracted from their LC-MS data and output in a comprehensive list. The developed model also allowed further insight into the composition of snake venom by highlighting the most relevant metabolites of each group by clustering similarly composed venoms. The model was created by means of support vector machines and used 20 features, which were merged into 10 principal components. All samples from the first and second validation data subsets were correctly classified. Biological hypotheses relevant to the variation regarding the metabolites that were identified are also given.
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Affiliation(s)
- Luis L. Alonso
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1012 WX Amsterdam, The Netherlands
| | - Julien Slagboom
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1012 WX Amsterdam, The Netherlands
| | - Nicholas R. Casewell
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Saer Samanipour
- Van ‘t Hof Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Jeroen Kool
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1012 WX Amsterdam, The Netherlands
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van Thiel J, Alonso LL, Slagboom J, Dunstan N, Wouters RM, Modahl CM, Vonk FJ, Jackson TNW, Kool J. Highly Evolvable: Investigating Interspecific and Intraspecific Venom Variation in Taipans ( Oxyuranus spp.) and Brown Snakes ( Pseudonaja spp.). Toxins (Basel) 2023; 15:74. [PMID: 36668892 PMCID: PMC9864820 DOI: 10.3390/toxins15010074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 01/14/2023] Open
Abstract
Snake venoms are complex mixtures of toxins that differ on interspecific (between species) and intraspecific (within species) levels. Whether venom variation within a group of closely related species is explained by the presence, absence and/or relative abundances of venom toxins remains largely unknown. Taipans (Oxyuranus spp.) and brown snakes (Pseudonaja spp.) represent medically relevant species of snakes across the Australasian region and provide an excellent model clade for studying interspecific and intraspecific venom variation. Using liquid chromatography with ultraviolet and mass spectrometry detection, we analyzed a total of 31 venoms covering all species of this monophyletic clade, including widespread localities. Our results reveal major interspecific and intraspecific venom variation in Oxyuranus and Pseudonaja species, partially corresponding with their geographical regions and phylogenetic relationships. This extensive venom variability is generated by a combination of the absence/presence and differential abundance of venom toxins. Our study highlights that venom systems can be highly dynamical on the interspecific and intraspecific levels and underscores that the rapid toxin evolvability potentially causes major impacts on neglected tropical snakebites.
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Affiliation(s)
- Jory van Thiel
- Division of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
- Naturalis Biodiversity Center, 2333 CR Leiden, The Netherlands
| | - Luis L. Alonso
- Division of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1012 WX Amsterdam, The Netherlands
| | - Julien Slagboom
- Division of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1012 WX Amsterdam, The Netherlands
| | | | - Roel M. Wouters
- Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Cassandra M. Modahl
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Freek J. Vonk
- Division of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Naturalis Biodiversity Center, 2333 CR Leiden, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1012 WX Amsterdam, The Netherlands
| | - Timothy N. W. Jackson
- Australian Venom Research Unit, Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jeroen Kool
- Division of Bioanalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), 1012 WX Amsterdam, The Netherlands
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Abstract
The inter-observer reliability and accuracy of the tongue blade test (TBT) for the identification of patients with mandibular fracture was prospectively evaluated using radiographic diagnosis as the gold standard. A consecutive sample of 110 patients presenting to the emergency department of a teaching county hospital was studied. Patients with uninterpretable x-rays, known diagnosis of mandibular fracture, or inability to cooperate for the test were excluded. Bilateral ability to crack a wooden tongue blade held between the teeth was scored as a negative test. Fifty-three patients had mandibular fractures. In the study group, the TBT had a sensitivity of 95.7%; a specificity of 63.5%; a positive predictive value of 66.2%; a negative predictive value of 95.2%; and an accuracy of 77.3%. The TBT provided contributory evidence useful in screening patients for mandibular fracture.
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Affiliation(s)
- L L Alonso
- Department of Emergency Medicine, Kern Medical Center, Bakersfield, California 93305, USA
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