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Jabri A, Khan J, Taftafa B, Alsharif M, Mhannayeh A, Chinnappan R, Alzhrani A, Kazmi S, Mir MS, Alsaud AW, Yaqinuddin A, Assiri AM, AlKattan K, Vashist YK, Broering DC, Mir TA. Bioengineered Organoids Offer New Possibilities for Liver Cancer Studies: A Review of Key Milestones and Challenges. Bioengineering (Basel) 2024; 11:346. [PMID: 38671768 PMCID: PMC11048289 DOI: 10.3390/bioengineering11040346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Hepatic cancer is widely regarded as the leading cause of cancer-related mortality worldwide. Despite recent advances in treatment options, the prognosis of liver cancer remains poor. Therefore, there is an urgent need to develop more representative in vitro models of liver cancer for pathophysiology and drug screening studies. Fortunately, an exciting new development for generating liver models in recent years has been the advent of organoid technology. Organoid models hold huge potential as an in vitro research tool because they can recapitulate the spatial architecture of primary liver cancers and maintain the molecular and functional variations of the native tissue counterparts during long-term culture in vitro. This review provides a comprehensive overview and discussion of the establishment and application of liver organoid models in vitro. Bioengineering strategies used to construct organoid models are also discussed. In addition, the clinical potential and other relevant applications of liver organoid models in different functional states are explored. In the end, this review discusses current limitations and future prospects to encourage further development.
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Affiliation(s)
- Abdullah Jabri
- College of Medicine, Alfaisal University, Riyadh 11211, Saudi Arabia (R.C.); (A.W.A.); (K.A.)
| | - Jibran Khan
- College of Medicine, Alfaisal University, Riyadh 11211, Saudi Arabia (R.C.); (A.W.A.); (K.A.)
| | - Bader Taftafa
- College of Medicine, Alfaisal University, Riyadh 11211, Saudi Arabia (R.C.); (A.W.A.); (K.A.)
| | - Mohamed Alsharif
- College of Medicine, Alfaisal University, Riyadh 11211, Saudi Arabia (R.C.); (A.W.A.); (K.A.)
| | - Abdulaziz Mhannayeh
- College of Medicine, Alfaisal University, Riyadh 11211, Saudi Arabia (R.C.); (A.W.A.); (K.A.)
| | - Raja Chinnappan
- College of Medicine, Alfaisal University, Riyadh 11211, Saudi Arabia (R.C.); (A.W.A.); (K.A.)
- Tissue/Organ Bioengineering and BioMEMS Lab, Organ Transplant Centre of Excellence (TR&I Dpt), King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Alaa Alzhrani
- College of Medicine, Alfaisal University, Riyadh 11211, Saudi Arabia (R.C.); (A.W.A.); (K.A.)
- Tissue/Organ Bioengineering and BioMEMS Lab, Organ Transplant Centre of Excellence (TR&I Dpt), King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21423, Saudi Arabia
| | - Shadab Kazmi
- Tissue/Organ Bioengineering and BioMEMS Lab, Organ Transplant Centre of Excellence (TR&I Dpt), King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
- Pathology and laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mohammad Shabab Mir
- School of Pharmacy, Desh Bhagat University, Mandi Gobindgarh 147301, Punjab, India;
| | - Aljohara Waleed Alsaud
- College of Medicine, Alfaisal University, Riyadh 11211, Saudi Arabia (R.C.); (A.W.A.); (K.A.)
| | - Ahmed Yaqinuddin
- College of Medicine, Alfaisal University, Riyadh 11211, Saudi Arabia (R.C.); (A.W.A.); (K.A.)
| | - Abdullah M. Assiri
- College of Medicine, Alfaisal University, Riyadh 11211, Saudi Arabia (R.C.); (A.W.A.); (K.A.)
- Tissue/Organ Bioengineering and BioMEMS Lab, Organ Transplant Centre of Excellence (TR&I Dpt), King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Khaled AlKattan
- College of Medicine, Alfaisal University, Riyadh 11211, Saudi Arabia (R.C.); (A.W.A.); (K.A.)
- Tissue/Organ Bioengineering and BioMEMS Lab, Organ Transplant Centre of Excellence (TR&I Dpt), King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Yogesh K. Vashist
- Tissue/Organ Bioengineering and BioMEMS Lab, Organ Transplant Centre of Excellence (TR&I Dpt), King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Dieter C. Broering
- College of Medicine, Alfaisal University, Riyadh 11211, Saudi Arabia (R.C.); (A.W.A.); (K.A.)
- Tissue/Organ Bioengineering and BioMEMS Lab, Organ Transplant Centre of Excellence (TR&I Dpt), King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Tanveer Ahmad Mir
- College of Medicine, Alfaisal University, Riyadh 11211, Saudi Arabia (R.C.); (A.W.A.); (K.A.)
- Tissue/Organ Bioengineering and BioMEMS Lab, Organ Transplant Centre of Excellence (TR&I Dpt), King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
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Wu Y, Wang C, Fan X, Ma Y, Liu Z, Ye X, Shen C, Wu C. The impact of induced pluripotent stem cells in animal conservation. Vet Res Commun 2024; 48:649-663. [PMID: 38228922 DOI: 10.1007/s11259-024-10294-3] [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: 11/02/2023] [Accepted: 01/04/2024] [Indexed: 01/18/2024]
Abstract
It is widely acknowledged that we are currently facing a critical tipping point with regards to global extinction, with human activities driving us perilously close to the brink of a devastating sixth mass extinction. As a promising option for safeguarding endangered species, induced pluripotent stem cells (iPSCs) hold great potential to aid in the preservation of threatened animal populations. For endangered species, such as the northern white rhinoceros (Ceratotherium simum cottoni), supply of embryos is often limited. After the death of the last male in 2019, only two females remained in the world. IPSC technology offers novel approaches and techniques for obtaining pluripotent stem cells (PSCs) from rare and endangered animal species. Successful generation of iPSCs circumvents several bottlenecks that impede the development of PSCs, including the challenges associated with establishing embryonic stem cells, limited embryo sources and immune rejection following embryo transfer. To provide more opportunities and room for growth in our work on animal welfare, in this paper we will focus on the progress made with iPSC lines derived from endangered and extinct species, exploring their potential applications and limitations in animal welfare research.
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Affiliation(s)
- Yurou Wu
- School of Pharmacy/School of Modem Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, People's Republic of China
| | - Chengwei Wang
- School of Pharmacy/School of Modem Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, People's Republic of China
| | - Xinyun Fan
- School of Pharmacy/School of Modem Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, People's Republic of China
| | - Yuxiao Ma
- Department of Biology, New York University, New York, NY, USA
| | - Zibo Liu
- School of Pharmacy/School of Modem Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, People's Republic of China
| | - Xun Ye
- School of Pharmacy/School of Modem Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, People's Republic of China
| | - Chongyang Shen
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People's Republic of China.
| | - Chunjie Wu
- Innovative Institute of Chinese Medicine and Pharmacy/Academy for Interdiscipline, Chengdu Univesity of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People's Republic of China.
- Sichuan Engineering Research Center for Endangered Medicinal Animals, Chengdu, China.
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3
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Zdyrski C, Gabriel V, Gessler TB, Ralston A, Sifuentes-Romero I, Kundu D, Honold S, Wickham H, Topping NE, Sahoo DK, Bista B, Tamplin J, Ospina O, Piñeyro P, Arriaga M, Galan JA, Meyerholz DK, Allenspach K, Mochel JP, Valenzuela N. Establishment and characterization of turtle liver organoids provides a potential model to decode their unique adaptations. Commun Biol 2024; 7:218. [PMID: 38388772 PMCID: PMC10883927 DOI: 10.1038/s42003-024-05818-1] [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: 09/27/2023] [Accepted: 01/15/2024] [Indexed: 02/24/2024] Open
Abstract
Painted turtles are remarkable for their freeze tolerance and supercooling ability along with their associated resilience to hypoxia/anoxia and oxidative stress, rendering them an ideal biomedical model for hypoxia-induced injuries (including strokes), tissue cooling during surgeries, and organ cryopreservation. Yet, such research is hindered by their seasonal reproduction and slow maturation. Here we developed and characterized adult stem cell-derived turtle liver organoids (3D self-assembled in vitro structures) from painted, snapping, and spiny softshell turtles spanning ~175My of evolution, with a subset cryopreserved. This development is, to the best of our knowledge, a first for this vertebrate Order, and complements the only other non-avian reptile organoids from snake venom glands. Preliminary characterization, including morphological, transcriptomic, and proteomic analyses, revealed organoids enriched in cholangiocytes. Deriving organoids from distant turtles and life stages demonstrates that our techniques are broadly applicable to chelonians, permitting the development of functional genomic tools currently lacking in herpetological research. Such platform could potentially support studies including genome-to-phenome mapping, gene function, genome architecture, and adaptive responses to climate change, with implications for ecological, evolutionary, and biomedical research.
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Affiliation(s)
- Christopher Zdyrski
- SMART Pharmacology, Department of Biomedical Sciences, Iowa State University, Ames, IA, USA.
- 3D Health Solutions Inc., Ames, IA, USA.
- SMART Pharmacology, Precision One Health Initiative, University of Georgia, Athens, GA, USA.
| | - Vojtech Gabriel
- SMART Pharmacology, Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
| | - Thea B Gessler
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | | | - Itzel Sifuentes-Romero
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Debosmita Kundu
- Department of Statistics, Iowa State University, Ames, IA, USA
| | - Sydney Honold
- SMART Pharmacology, Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
| | - Hannah Wickham
- SMART Pharmacology, Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
| | - Nicholas E Topping
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Dipak Kumar Sahoo
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, IA, USA
| | - Basanta Bista
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Jeffrey Tamplin
- Department of Biology, University of Northern Iowa, Cedar Falls, IA, USA
| | - Oscar Ospina
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Pablo Piñeyro
- Veterinary Diagnostic Laboratory, Iowa State University, Ames, IA, USA
| | - Marco Arriaga
- Department of Human Genetics, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Jacob A Galan
- Department of Human Genetics, University of Texas Rio Grande Valley, Brownsville, TX, USA
| | | | - Karin Allenspach
- SMART Pharmacology, Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
- 3D Health Solutions Inc., Ames, IA, USA
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, IA, USA
- SMART Pharmacology, Precision One Health Initiative, University of Georgia, Athens, GA, USA
| | - Jonathan P Mochel
- SMART Pharmacology, Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
- 3D Health Solutions Inc., Ames, IA, USA
- SMART Pharmacology, Precision One Health Initiative, University of Georgia, Athens, GA, USA
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA.
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Modahl CM, Han SX, van Thiel J, Vaz C, Dunstan NL, Frietze S, Jackson TNW, Mackessy SP, Kini RM. Distinct regulatory networks control toxin gene expression in elapid and viperid snakes. BMC Genomics 2024; 25:186. [PMID: 38365592 PMCID: PMC10874052 DOI: 10.1186/s12864-024-10090-y] [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: 07/28/2023] [Accepted: 02/05/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Venom systems are ideal models to study genetic regulatory mechanisms that underpin evolutionary novelty. Snake venom glands are thought to share a common origin, but there are major distinctions between venom toxins from the medically significant snake families Elapidae and Viperidae, and toxin gene regulatory investigations in elapid snakes have been limited. Here, we used high-throughput RNA-sequencing to profile gene expression and microRNAs between active (milked) and resting (unmilked) venom glands in an elapid (Eastern Brown Snake, Pseudonaja textilis), in addition to comparative genomics, to identify cis- and trans-acting regulation of venom production in an elapid in comparison to viperids (Crotalus viridis and C. tigris). RESULTS Although there is conservation in high-level mechanistic pathways regulating venom production (unfolded protein response, Notch signaling and cholesterol homeostasis), there are differences in the regulation of histone methylation enzymes, transcription factors, and microRNAs in venom glands from these two snake families. Histone methyltransferases and transcription factor (TF) specificity protein 1 (Sp1) were highly upregulated in the milked elapid venom gland in comparison to the viperids, whereas nuclear factor I (NFI) TFs were upregulated after viperid venom milking. Sp1 and NFI cis-regulatory elements were common to toxin gene promoter regions, but many unique elements were also present between elapid and viperid toxins. The presence of Sp1 binding sites across multiple elapid toxin gene promoter regions that have been experimentally determined to regulate expression, in addition to upregulation of Sp1 after venom milking, suggests this transcription factor is involved in elapid toxin expression. microRNA profiles were distinctive between milked and unmilked venom glands for both snake families, and microRNAs were predicted to target a diversity of toxin transcripts in the elapid P. textilis venom gland, but only snake venom metalloproteinase transcripts in the viperid C. viridis venom gland. These results suggest differences in toxin gene posttranscriptional regulation between the elapid P. textilis and viperid C. viridis. CONCLUSIONS Our comparative transcriptomic and genomic analyses between toxin genes and isoforms in elapid and viperid snakes suggests independent toxin regulation between these two snake families, demonstrating multiple different regulatory mechanisms underpin a venomous phenotype.
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Affiliation(s)
- Cassandra M Modahl
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore.
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, U.K..
| | - Summer Xia Han
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
- Fulcrum Therapeutics, Cambridge, MA, U.S.A
| | - Jory van Thiel
- Centre for Snakebite Research and Interventions, Liverpool School of Tropical Medicine, Liverpool, U.K
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Candida Vaz
- Human Development, Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | | | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT, U.S.A
| | - Timothy N W Jackson
- Australian Venom Research Unit, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Australia
| | - Stephen P Mackessy
- Department of Biological Sciences, University of Northern Colorado, Greeley, CO, U.S.A
| | - R Manjunatha Kini
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore.
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Singapore Eye Research Institute, Singapore, Singapore.
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, U.S.A..
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Ye F, Wang J, Li J, Mei Y, Guo G. Mapping Cell Atlases at the Single-Cell Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305449. [PMID: 38145338 PMCID: PMC10885669 DOI: 10.1002/advs.202305449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/01/2023] [Indexed: 12/26/2023]
Abstract
Recent advancements in single-cell technologies have led to rapid developments in the construction of cell atlases. These atlases have the potential to provide detailed information about every cell type in different organisms, enabling the characterization of cellular diversity at the single-cell level. Global efforts in developing comprehensive cell atlases have profound implications for both basic research and clinical applications. This review provides a broad overview of the cellular diversity and dynamics across various biological systems. In addition, the incorporation of machine learning techniques into cell atlas analyses opens up exciting prospects for the field of integrative biology.
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Affiliation(s)
- Fang Ye
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jingjing Wang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
| | - Jiaqi Li
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Yuqing Mei
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
| | - Guoji Guo
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative MedicineZhejiang University School of MedicineHangzhouZhejiang310000China
- Liangzhu LaboratoryZhejiang UniversityHangzhouZhejiang311121China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative MedicineDr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative MedicineHangzhouZhejiang310058China
- Institute of HematologyZhejiang UniversityHangzhouZhejiang310000China
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Gabriel V, Zdyrski C, Sahoo DK, Ralston A, Wickham H, Bourgois-Mochel A, Ahmed B, Merodio MM, Paukner K, Piñeyro P, Kopper J, Rowe EW, Smith JD, Meyerholz D, Kol A, Viall A, Elbadawy M, Mochel JP, Allenspach K. Adult Animal Stem Cell-Derived Organoids in Biomedical Research and the One Health Paradigm. Int J Mol Sci 2024; 25:701. [PMID: 38255775 PMCID: PMC10815683 DOI: 10.3390/ijms25020701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Preclinical biomedical research is limited by the predictiveness of in vivo and in vitro models. While in vivo models offer the most complex system for experimentation, they are also limited by ethical, financial, and experimental constraints. In vitro models are simplified models that do not offer the same complexity as living animals but do offer financial affordability and more experimental freedom; therefore, they are commonly used. Traditional 2D cell lines cannot fully simulate the complexity of the epithelium of healthy organs and limit scientific progress. The One Health Initiative was established to consolidate human, animal, and environmental health while also tackling complex and multifactorial medical problems. Reverse translational research allows for the sharing of knowledge between clinical research in veterinary and human medicine. Recently, organoid technology has been developed to mimic the original organ's epithelial microstructure and function more reliably. While human and murine organoids are available, numerous other organoids have been derived from traditional veterinary animals and exotic species in the last decade. With these additional organoid models, species previously excluded from in vitro research are becoming accessible, therefore unlocking potential translational and reverse translational applications of animals with unique adaptations that overcome common problems in veterinary and human medicine.
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Affiliation(s)
- Vojtech Gabriel
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (H.W.); (B.A.); (J.P.M.)
| | | | - Dipak K. Sahoo
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, IA 50011, USA; (D.K.S.); (A.B.-M.); (J.K.)
| | - Abigail Ralston
- 3D Health Solutions Inc., Ames, IA 50010, USA; (C.Z.); (A.R.); (M.M.M.)
| | - Hannah Wickham
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (H.W.); (B.A.); (J.P.M.)
| | - Agnes Bourgois-Mochel
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, IA 50011, USA; (D.K.S.); (A.B.-M.); (J.K.)
| | - Basant Ahmed
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (H.W.); (B.A.); (J.P.M.)
| | - Maria M. Merodio
- 3D Health Solutions Inc., Ames, IA 50010, USA; (C.Z.); (A.R.); (M.M.M.)
| | - Karel Paukner
- Atherosclerosis Research Laboratory, Centre for Experimental Medicine, Institute for Clinical and Experimental Medicine, 14021 Prague, Czech Republic;
| | - Pablo Piñeyro
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (P.P.); (J.D.S.)
| | - Jamie Kopper
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, IA 50011, USA; (D.K.S.); (A.B.-M.); (J.K.)
| | - Eric W. Rowe
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (H.W.); (B.A.); (J.P.M.)
| | - Jodi D. Smith
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (P.P.); (J.D.S.)
| | - David Meyerholz
- Department of Pathology, University of Iowa, Iowa City, IA 52242, USA;
| | - Amir Kol
- Department of Pathology, University of California, Davis, CA 94143, USA; (A.K.); (A.V.)
| | - Austin Viall
- Department of Pathology, University of California, Davis, CA 94143, USA; (A.K.); (A.V.)
| | - Mohamed Elbadawy
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30530, USA;
- Department of Pharmacology, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt
| | - Jonathan P. Mochel
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (H.W.); (B.A.); (J.P.M.)
- 3D Health Solutions Inc., Ames, IA 50010, USA; (C.Z.); (A.R.); (M.M.M.)
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30530, USA;
| | - Karin Allenspach
- 3D Health Solutions Inc., Ames, IA 50010, USA; (C.Z.); (A.R.); (M.M.M.)
- Department of Veterinary Clinical Sciences, Iowa State University, Ames, IA 50011, USA; (D.K.S.); (A.B.-M.); (J.K.)
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30530, USA;
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7
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Beumer J, Clevers H. Hallmarks of stemness in mammalian tissues. Cell Stem Cell 2024; 31:7-24. [PMID: 38181752 PMCID: PMC10769195 DOI: 10.1016/j.stem.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/03/2023] [Accepted: 12/08/2023] [Indexed: 01/07/2024]
Abstract
All adult tissues experience wear and tear. Most tissues can compensate for cell loss through the activity of resident stem cells. Although the cellular maintenance strategies vary greatly between different adult (read: postnatal) tissues, the function of stem cells is best defined by their capacity to replace lost tissue through division. We discuss a set of six complementary hallmarks that are key enabling features of this basic function. These include longevity and self-renewal, multipotency, transplantability, plasticity, dependence on niche signals, and maintenance of genome integrity. We discuss these hallmarks in the context of some of the best-understood adult stem cell niches.
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Affiliation(s)
- Joep Beumer
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Basel, Switzerland.
| | - Hans Clevers
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Basel, Switzerland.
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8
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Nachtigall PG, Durham AM, Rokyta DR, Junqueira-de-Azevedo ILM. ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages. Gigascience 2024; 13:giad116. [PMID: 38241143 PMCID: PMC10797961 DOI: 10.1093/gigascience/giad116] [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: 07/14/2023] [Revised: 10/19/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND The rapid development of sequencing technologies resulted in a wide expansion of genomics studies using venomous lineages. This facilitated research focusing on understanding the evolution of adaptive traits and the search for novel compounds that can be applied in agriculture and medicine. However, the toxin annotation of genomes is a laborious and time-consuming task, and no consensus pipeline is currently available. No computational tool currently exists to address the challenges specific to toxin annotation and to ensure the reproducibility of the process. RESULTS Here, we present ToxCodAn-Genome, the first software designed to perform automated toxin annotation in genomes of venomous lineages. This pipeline was designed to retrieve the full-length coding sequences of toxins and to allow the detection of novel truncated paralogs and pseudogenes. We tested ToxCodAn-Genome using 12 genomes of venomous lineages and achieved high performance on recovering their current toxin annotations. This tool can be easily customized to allow improvements in the final toxin annotation set and can be expanded to virtually any venomous lineage. ToxCodAn-Genome is fast, allowing it to run on any personal computer, but it can also be executed in multicore mode, taking advantage of large high-performance servers. In addition, we provide a guide to direct future research in the venomics field to ensure a confident toxin annotation in the genome being studied. As a case study, we sequenced and annotated the toxin repertoire of Bothrops alternatus, which may facilitate future evolutionary and biomedical studies using vipers as models. CONCLUSIONS ToxCodAn-Genome is suitable to perform toxin annotation in the genome of venomous species and may help to improve the reproducibility of further studies. ToxCodAn-Genome and the guide are freely available at https://github.com/pedronachtigall/ToxCodAn-Genome.
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Affiliation(s)
- Pedro G Nachtigall
- Laboratório de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, 05503-900 SP, Brazil
- Department of Biological Science, Florida State University, Tallahassee, 32306-4295 FL, USA
| | - Alan M Durham
- Departamento de Ciência da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo (USP), São Paulo, 05508-090 SP, Brazil
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, 32306-4295 FL, USA
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9
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Bai L, Wu Y, Li G, Zhang W, Zhang H, Su J. AI-enabled organoids: Construction, analysis, and application. Bioact Mater 2024; 31:525-548. [PMID: 37746662 PMCID: PMC10511344 DOI: 10.1016/j.bioactmat.2023.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/09/2023] [Accepted: 09/09/2023] [Indexed: 09/26/2023] Open
Abstract
Organoids, miniature and simplified in vitro model systems that mimic the structure and function of organs, have attracted considerable interest due to their promising applications in disease modeling, drug screening, personalized medicine, and tissue engineering. Despite the substantial success in cultivating physiologically relevant organoids, challenges remain concerning the complexities of their assembly and the difficulties associated with data analysis. The advent of AI-Enabled Organoids, which interfaces with artificial intelligence (AI), holds the potential to revolutionize the field by offering novel insights and methodologies that can expedite the development and clinical application of organoids. This review succinctly delineates the fundamental concepts and mechanisms underlying AI-Enabled Organoids, summarizing the prospective applications on rapid screening of construction strategies, cost-effective extraction of multiscale image features, streamlined analysis of multi-omics data, and precise preclinical evaluation and application. We also explore the challenges and limitations of interfacing organoids with AI, and discuss the future direction of the field. Taken together, the AI-Enabled Organoids hold significant promise for advancing our understanding of organ development and disease progression, ultimately laying the groundwork for clinical application.
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Affiliation(s)
- Long Bai
- Department of Orthopedics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
- Wenzhou Institute of Shanghai University, Wenzhou, 325000, China
| | - Yan Wu
- Department of Orthopedics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
| | - Guangfeng Li
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
- Department of Orthopedics, Shanghai Zhongye Hospital, Shanghai, 201941, China
| | - Wencai Zhang
- Department of Orthopedics, First Affiliated Hospital, Jinan University, Guangzhou, 510632, China
| | - Hao Zhang
- Department of Orthopedics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
| | - Jiacan Su
- Department of Orthopedics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
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10
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Theart F, Kemp L, Buys C, Hauptfleisch M, Berg P. A confirmed human fatality due to envenomation by the Kunene Coral Snake (Aspidelaps lubricus cowlesi) in Namibia. Toxicon 2024; 237:107537. [PMID: 38043715 DOI: 10.1016/j.toxicon.2023.107537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/05/2023]
Abstract
Shield-nose and Coral snakes (Aspidelaps spp.) are medium sized venomous snakes found throughout southern Africa. Little is known about the venom of these snakes and its clinical relevance, as human bites are uncommon. Neurological signs and symptoms usually develop following bites by this genus but evaluations of the severity are inconclusive. We report on the first confirmed human fatality by the Kunene Shield-nose Snake (Aspidelaps lubricus cowlesi) in a child. Envenomation by Aspidelaps and other snakes considered lesser-venomous - especially those possessing neurotoxic venom - should be treated with caution as they may result in life-threatening envenomation without established clinical management protocols.
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Affiliation(s)
- Francois Theart
- Namibia University of Science and Technology, 13 Jackson Kaujeua Street, Windhoek, Namibia.
| | - Luke Kemp
- African Snakebite Institute, Wapadrand, Pretoria, South Africa
| | - Christo Buys
- Namibian Snakebite Management Expert, Namibian Snakebite Interest Group, Windhoek, Namibia
| | - Morgan Hauptfleisch
- Namibia University of Science and Technology, 13 Jackson Kaujeua Street, Windhoek, Namibia
| | - Philipp Berg
- AfriMed e.V., Mühlheim, Germany; Erongo Park, Omaruru, Namibia.
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11
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Wu C, Li L, Wang Y, Wei S, Zhu J. Morphological, functional, compositional and transcriptional constraints shape the distinct venom profiles of the assassin bug Sycanus croceovittatus. Int J Biol Macromol 2023; 250:126162. [PMID: 37558034 DOI: 10.1016/j.ijbiomac.2023.126162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/11/2023]
Abstract
Predatory bugs employ a salivary venom apparatus to generate complex venoms for capturing and digesting prey. The venom apparatus consists of different glands for the production of distinct venom sets, but the underlying mechanisms behind this process remain poorly understood. Here we present a comprehensive analysis of the morphological, functional, compositional and transcriptional characteristics of venoms derived from posterior main gland (PMG), anterior main gland (AMG), and accessory gland (AG) of the assassin bug Sycanus croceovittatus. Structural observations revealed the intricate constructions of the venom apparatus, enabling the production and storage of three distinct venom sets in anatomically varied glands and allowing them to be modulated in a context-dependent manner upon utilization. There were remarkable differences in the biological activities exhibited by PMG, AMG, and AG venoms. Proteotranscriptomic analysis demonstrated that these venoms displayed compositional heterogeneity at both the quantity and variety levels of proteins. Transcriptional profiles of the identified venom proteins revealed gland-specific or biased expression patterns. These findings indicate that the divergence in venom profiles among different glands arises from morphological, functional, compositional and transcriptional constraints on the venom apparatus, reflecting remarkable morphogenesis and regulatory gene networks responsible for the compartmentalized production of venom proteins in different glands.
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Affiliation(s)
- Chaoyan Wu
- Key Laboeratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Lu Li
- Key Laboeratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Yuqin Wang
- Key Laboeratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Shujun Wei
- Key Laboeratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China; Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jiaying Zhu
- Key Laboeratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China; Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China.
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12
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Szabó L, Seubert AC, Kretzschmar K. Modelling adult stem cells and their niche in health and disease with epithelial organoids. Semin Cell Dev Biol 2023; 144:20-30. [PMID: 36127261 DOI: 10.1016/j.semcdb.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 10/14/2022]
Abstract
Adult stem cells are responsible for homoeostasis and regeneration of epithelial tissues. Stem cell function is regulated by both cell autonomous mechanisms as well as the niche. Deregulated stem cell function contributes to diseases such as cancer. Epithelial organoid cultures generated from tissue-resident adult stem cells have allowed unprecedented insights into the biology of epithelial tissues. The subsequent adaptation of organoid technology enabled the modelling of the communication of stem cells with their cellular and non-cellular niche as well as diseases. Starting from its first model described in 2009, the murine small intestinal organoid, we discuss here how epithelial organoid cultures have been become a prime in vitro research tool for cell and developmental biology, bioengineering, and biomedicine in the last decade.
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Affiliation(s)
- Lili Szabó
- Mildred Scheel Early Career Centre (MSNZ) for Cancer Research, University Hospital Würzburg, IZKF/MSNZ, Würzburg, Germany
| | - Anna C Seubert
- Mildred Scheel Early Career Centre (MSNZ) for Cancer Research, University Hospital Würzburg, IZKF/MSNZ, Würzburg, Germany
| | - Kai Kretzschmar
- Mildred Scheel Early Career Centre (MSNZ) for Cancer Research, University Hospital Würzburg, IZKF/MSNZ, Würzburg, Germany.
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13
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Ong KJ, Tejeda-Saldana Y, Duffy B, Holmes D, Kukk K, Shatkin JA. Cultured Meat Safety Research Priorities: Regulatory and Governmental Perspectives. Foods 2023; 12:2645. [PMID: 37509737 PMCID: PMC10379195 DOI: 10.3390/foods12142645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/23/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
As with every new technology, safety demonstration is a critical component of bringing products to market and gaining public acceptance for cultured meat and seafood. This manuscript develops research priorities from the findings of a series of interviews and workshops with governmental scientists and regulators from food safety agencies in fifteen jurisdictions globally. The interviews and workshops aimed to identify the key safety questions and priority areas of research. Participants raised questions about which aspects of cultured meat and seafood production are novel, and the implications of the paucity of public information on the topic. Novel parameters and targets may require the development of new analytical methods or adaptation and validation of existing ones, including for a diversity of product types and processes. Participants emphasized that data sharing of these efforts would be valuable, similar to those already developed and used in the food and pharmaceutical fields. Contributions to such databases from the private and public sectors would speed general understanding as well as efforts to make evaluations more efficient. In turn, these resources, combined with transparent risk assessment, will be critical elements of building consumer trust in cultured meat and seafood products.
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Affiliation(s)
| | | | | | - Dwayne Holmes
- Stichting New Harvest Netherlands, 1052 Amsterdam, The Netherlands
| | - Kora Kukk
- Vireo Advisors, LLC, Boston, MA 02130, USA
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14
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Torrejón D, Cárdenas J, Juárez D, Espinoza J, Proleón A, Agurto-Arteaga A, Lazo F, Leguía M, Urra FA, Sánchez EF, Chávez-Olortegui C, Vivas-Ruiz DE, Yarlequé A. Comparison of Four Methods of RNA Extraction and cDNA Synthesis from The Venom of Peruvian Snakes of the Genus Bothrops of Clinical Importance. Int J Mol Sci 2023; 24:11161. [PMID: 37446341 DOI: 10.3390/ijms241311161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
RNA purification and cDNA synthesis represents the starting point for molecular analyses of snake venom proteins-enzymes. Usually, the sacrifice of snakes is necessary for venom gland extraction to identify protein-coding transcripts; however, the venom can be used as a source of transcripts. Although there are methods for obtaining RNA from venom, no comparative analysis has been conducted in the Bothrops genus. In the present study, we compared four commercial methods for RNA purification and cDNA synthesis from venom (liquid, lyophilized, or long-term storage) of four clinically relevant species of Peruvian Bothrops. Our results show that the TRIzol method presents the highest yield of RNA purified from venom (59 ± 11 ng/100 µL or 10 mg). The SuperScript First-Strand Synthesis System kit produced high amounts of cDNA (3.2 ± 1.2 ng cDNA/ng RNA), and the highest value was from combination with the Dynabeads mRNA DIRECT kit (4.8 ± 2.0 ng cDNA/ng RNA). The utility of cDNA was demonstrated with the amplification of six relevant toxins: thrombin-like enzymes, P-I and P-III metalloproteinases, acid and basic phospholipases A2, and disintegrins. To our knowledge, this is the first comparative study of RNA purification and cDNA synthesis methodologies from Bothrops genus venom.
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Affiliation(s)
- Daniel Torrejón
- Laboratorio de Biología Molecular, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima Cercado, Lima 15081, Peru
| | - Javier Cárdenas
- Laboratorio de Bioquímica, Facultad de Ciencias de la Salud, Universidad Nacional del del Callao, Av. Juan Pablo ΙΙ 306, Bellavista 07011, Peru
| | - Diana Juárez
- Laboratorio de Genómica, Pontificia Universidad Católica del Perú, Av. Universitaria 1801, Campus Principal, San Miguel 15088, Peru
| | - Jordano Espinoza
- Laboratorio de Biología Molecular, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima Cercado, Lima 15081, Peru
| | - Alex Proleón
- Laboratorio de Biología Molecular, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima Cercado, Lima 15081, Peru
| | - Andrés Agurto-Arteaga
- Laboratorio de Biología Molecular, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima Cercado, Lima 15081, Peru
| | - Fanny Lazo
- Laboratorio de Biología Molecular, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima Cercado, Lima 15081, Peru
| | - Mariana Leguía
- Laboratorio de Genómica, Pontificia Universidad Católica del Perú, Av. Universitaria 1801, Campus Principal, San Miguel 15088, Peru
| | - Félix A Urra
- Laboratorio de Plasticidad Metabólica y Bioenergética, Programa de Farmacología Clínica y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile
- Network for Snake Venom Research and Drug Discovery, Av. Independencia 1027, Santiago 7810000, Chile
| | - Eladio F Sánchez
- Network for Snake Venom Research and Drug Discovery, Av. Independencia 1027, Santiago 7810000, Chile
- Research and Development Center, Ezequiel Dias Foundation, Belo Horizonte 30510-010, Minas Gerais, Brazil
| | - Carlos Chávez-Olortegui
- Departamento de Bioquímica-Inmunología, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Minas Gerais, Brazil
| | - Dan E Vivas-Ruiz
- Laboratorio de Biología Molecular, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima Cercado, Lima 15081, Peru
- Network for Snake Venom Research and Drug Discovery, Av. Independencia 1027, Santiago 7810000, Chile
| | - Armando Yarlequé
- Laboratorio de Biología Molecular, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Venezuela Cdra 34 S/N, Ciudad Universitaria, Lima Cercado, Lima 15081, Peru
- Network for Snake Venom Research and Drug Discovery, Av. Independencia 1027, Santiago 7810000, Chile
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15
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Tan Y, Martin TG, Harrison BC, Leinwand LA. Utility of the burmese Python as a model for studying plasticity of extreme physiological systems. J Muscle Res Cell Motil 2023; 44:95-106. [PMID: 36316565 PMCID: PMC10149580 DOI: 10.1007/s10974-022-09632-2] [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: 03/11/2022] [Accepted: 08/30/2022] [Indexed: 03/18/2023]
Abstract
Non-traditional animal models present an opportunity to discover novel biology that has evolved to allow such animals to survive in extreme environments. One striking example is the Burmese python (Python molurus bivittatus), which exhibits extreme physiological adaptation in various metabolic organs after consuming a large meal following long periods of fasting. The response to such a large meal in pythons involves a dramatic surge in metabolic rate, lipid overload in plasma, and massive but reversible organ growth through the course of digestion. Multiple studies have reported the physiological responses in post-prandial pythons, while the specific molecular control of these processes is less well-studied. Investigating the mechanisms that coordinate organ growth and adaptive responses offers the opportunity to gain novel insight that may be able to treat various pathologies in humans. Here, we summarize past research on the post-prandial physiological changes in the Burmese python with a focus on the gastrointestinal tract, heart, and liver. Specifically, we address our recent molecular discoveries in the post-prandial python liver which demonstrate transient adaptations that may reveal new therapeutic targets. Lastly, we explore new biology of the aquaporin 7 gene that is potently upregulated in mammalian cardiac myocytes by circulating factors in post-prandial python plasma.
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Affiliation(s)
- Yuxiao Tan
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado, Boulder. 3415 Colorado Ave, UCB 596, 80309, Boulder, CO, USA
| | - Thomas G Martin
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado, Boulder. 3415 Colorado Ave, UCB 596, 80309, Boulder, CO, USA
| | - Brooke C Harrison
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado, Boulder. 3415 Colorado Ave, UCB 596, 80309, Boulder, CO, USA
| | - Leslie A Leinwand
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado, Boulder. 3415 Colorado Ave, UCB 596, 80309, Boulder, CO, USA.
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16
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Quan YZ, Wei W, Ergin V, Rameshbabu A, Huang M, Tian C, Saladi S, Indzhykulian A, Chen ZY. Reprogramming by drug-like molecules leads to regeneration of cochlear hair cell-like cells in adult mice. Proc Natl Acad Sci U S A 2023; 120:e2215253120. [PMID: 37068229 PMCID: PMC10151514 DOI: 10.1073/pnas.2215253120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 03/02/2023] [Indexed: 04/19/2023] Open
Abstract
Strategies to overcome irreversible cochlear hair cell (HC) damage and loss in mammals are of vital importance to hearing recovery in patients with permanent hearing loss. In mature mammalian cochlea, co-activation of Myc and Notch1 reprograms supporting cells (SC) and promotes HC regeneration. Understanding of the underlying mechanisms may aid the development of a clinically relevant approach to achieve HC regeneration in the nontransgenic mature cochlea. By single-cell RNAseq, we show that MYC/NICD "rejuvenates" the adult mouse cochlea by activating multiple pathways including Wnt and cyclase activator of cyclic AMP (cAMP), whose blockade suppresses HC-like cell regeneration despite Myc/Notch activation. We screened and identified a combination (the cocktail) of drug-like molecules composing of small molecules and small interfering RNAs to activate the pathways of Myc, Notch1, Wnt and cAMP. We show that the cocktail effectively replaces Myc and Notch1 transgenes and reprograms fully mature wild-type (WT) SCs for HC-like cells regeneration in vitro. Finally, we demonstrate the cocktail is capable of reprogramming adult cochlea for HC-like cells regeneration in WT mice with HC loss in vivo. Our study identifies a strategy by a clinically relevant approach to reprogram mature inner ear for HC-like cells regeneration, laying the foundation for hearing restoration by HC regeneration.
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Affiliation(s)
- Yi-Zhou Quan
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA02115
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Neuroscience, Harvard Medical School, Boston, MA02115
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, MA02114
| | - Wei Wei
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA02115
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Neuroscience, Harvard Medical School, Boston, MA02115
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, MA02114
- Department of Otolaryngology-Head and Necks, Shengjing Hospital of China Medical University, Shenyang110004, China
| | - Volkan Ergin
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA02115
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Neuroscience, Harvard Medical School, Boston, MA02115
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, MA02114
| | - Arun Prabhu Rameshbabu
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA02115
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Neuroscience, Harvard Medical School, Boston, MA02115
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, MA02114
| | - Mingqian Huang
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA02115
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Neuroscience, Harvard Medical School, Boston, MA02115
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, MA02114
| | - Chunjie Tian
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA02115
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Neuroscience, Harvard Medical School, Boston, MA02115
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, MA02114
| | - Srinivas Vinod Saladi
- Broad Institute of MIT and Harvard, Cambridge, MA02142
- Department of Otolaryngology Head and Neck Surgery, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA02114
| | - Artur A. Indzhykulian
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA02115
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Neuroscience, Harvard Medical School, Boston, MA02115
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, MA02114
| | - Zheng-Yi Chen
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA02115
- Department of Otolaryngology-Head and Neck Surgery, Graduate Program in Neuroscience, Harvard Medical School, Boston, MA02115
- Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, MA02114
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17
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Future regenerative medicine developments and their therapeutic applications. Biomed Pharmacother 2023; 158:114131. [PMID: 36538861 DOI: 10.1016/j.biopha.2022.114131] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Although the currently available pharmacological assays can cure most pathological disorders, they have limited therapeutic value in relieving certain disorders like myocardial infarct, peripheral vascular disease, amputated limbs, or organ failure (e.g. renal failure). Pilot studies to overcome such problems using regenerative medicine (RM) delivered promising data. Comprehensive investigations of RM in zebrafish or reptilians are necessary for better understanding. However, the precise mechanisms remain poorly understood despite the tremendous amount of data obtained using the zebrafish model investigating the exact mechanisms behind their regenerative capability. Indeed, understanding such mechanisms and their application to humans can save millions of lives from dying due to potentially life-threatening events. Recent studies have launched a revolution in replacing damaged human organs via different approaches in the last few decades. The newly established branch of medicine (known as Regenerative Medicine aims to enhance natural repair mechanisms. This can be done through the application of several advanced broad-spectrum technologies such as organ transplantation, tissue engineering, and application of Scaffolds technology (support vascularization using an extracellular matrix), stem cell therapy, miRNA treatment, development of 3D mini-organs (organoids), and the construction of artificial tissues using nanomedicine and 3D bio-printers. Moreover, in the next few decades, revolutionary approaches in regenerative medicine will be applied based on artificial intelligence and wireless data exchange, soft intelligence biomaterials, nanorobotics, and even living robotics capable of self-repair. The present work presents a comprehensive overview that summarizes the new and future advances in the field of RM.
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18
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Lüddecke T, Paas A, Harris RJ, Talmann L, Kirchhoff KN, Billion A, Hardes K, Steinbrink A, Gerlach D, Fry BG, Vilcinskas A. Venom biotechnology: casting light on nature's deadliest weapons using synthetic biology. Front Bioeng Biotechnol 2023; 11:1166601. [PMID: 37207126 PMCID: PMC10188951 DOI: 10.3389/fbioe.2023.1166601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/18/2023] [Indexed: 05/21/2023] Open
Abstract
Venoms are complex chemical arsenals that have evolved independently many times in the animal kingdom. Venoms have attracted the interest of researchers because they are an important innovation that has contributed greatly to the evolutionary success of many animals, and their medical relevance offers significant potential for drug discovery. During the last decade, venom research has been revolutionized by the application of systems biology, giving rise to a novel field known as venomics. More recently, biotechnology has also made an increasing impact in this field. Its methods provide the means to disentangle and study venom systems across all levels of biological organization and, given their tremendous impact on the life sciences, these pivotal tools greatly facilitate the coherent understanding of venom system organization, development, biochemistry, and therapeutic activity. Even so, we lack a comprehensive overview of major advances achieved by applying biotechnology to venom systems. This review therefore considers the methods, insights, and potential future developments of biotechnological applications in the field of venom research. We follow the levels of biological organization and structure, starting with the methods used to study the genomic blueprint and genetic machinery of venoms, followed gene products and their functional phenotypes. We argue that biotechnology can answer some of the most urgent questions in venom research, particularly when multiple approaches are combined together, and with other venomics technologies.
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Affiliation(s)
- Tim Lüddecke
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- *Correspondence: Tim Lüddecke,
| | - Anne Paas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Richard J. Harris
- Venom Evolution Lab, School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Biosciences (IMB), The University of Queensland, Brisbane, QLD, Australia
| | - Lea Talmann
- Syngenta Crop Protection, Stein, Switzerland
| | - Kim N. Kirchhoff
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - André Billion
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Kornelia Hardes
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- BMBF Junior Research Group in Infection Research “ASCRIBE”, Giessen, Germany
| | - Antje Steinbrink
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Institute for Insect Biotechnology, Justus Liebig University of Giessen, Giessen, Germany
| | - Doreen Gerlach
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Bryan G. Fry
- Venom Evolution Lab, School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Institute for Insect Biotechnology, Justus Liebig University of Giessen, Giessen, Germany
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19
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Avella I, Wüster W, Luiselli L, Martínez-Freiría F. Toxic Habits: An Analysis of General Trends and Biases in Snake Venom Research. Toxins (Basel) 2022; 14:toxins14120884. [PMID: 36548781 PMCID: PMC9783912 DOI: 10.3390/toxins14120884] [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: 11/03/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Biases in snake venom research have been partially identified but seldomly quantified. Using the Google Scholar web search engine, we collected a total of 267 articles published between 1964 and 2021, and reviewed them to assess the main trends in this field of study. We developed a 4-category classification of the harmful potential of each of the 298 snake species retrieved from the analysed publications, and tested whether taxonomy, realm of origin, and/or assigned hazard category could affect how often each of them appeared in the articles considered. Overall, viperids were significantly more represented than any other snake taxon retrieved. The Neotropics were the most represented biogeographic realm for number of studied species, whereas information about the country of origin of the analysed specimens was often incomplete. The vast majority of the publications focused on snake venom characterisation, whereas more ecology-related topics were rarely considered. Hazard category and biogeographic realm of origin of each species had a significant effect on the number of articles dedicated to it, suggesting that a snake's harmful potential and place of origin influence its popularity in venom studies. Our analysis showed an overall positive trend in the number of snake venom studies published yearly, but also underlined severe neglect of snake families of supposedly minor medical relevance (e.g., Atractaspididae), underrepresentation of some of the areas most impacted by snakebite (i.e., Indomalayan and Afrotropic realms), and limited interest in the ecological and functional context of snake venom.
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Affiliation(s)
- Ignazio Avella
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
- Correspondence:
| | - Wolfgang Wüster
- Molecular Ecology and Evolution at Bangor, School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
| | - Luca Luiselli
- Institute for Development, Ecology, Conservation & Cooperation, Via G. Tomasi di Lampedusa 33, I-00144 Rome, Italy
- Department of Zoology, University of Lomé, Lomé 01BP1515, Togo
- Department of Environmental and Applied Biology, Rivers State University of Science and Technology, Port Harcourt P.M.B. 5080, Nigeria
| | - Fernando Martínez-Freiría
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
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20
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Paramore SV, Goodwin K, Nelson CM. How to build an epithelial tree. Phys Biol 2022; 19. [DOI: 10.1088/1478-3975/ac9e38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022]
Abstract
Abstract
Nature has evolved a variety of mechanisms to build epithelial trees of diverse architectures within different organs and across species. Epithelial trees are elaborated through branch initiation and extension, and their morphogenesis ends with branch termination. Each of these steps of the branching process can be driven by the actions of epithelial cells themselves (epithelial-intrinsic mechanisms) or by the cells of their surrounding tissues (epithelial-extrinsic mechanisms). Here, we describe examples of how these mechanisms drive each stage of branching morphogenesis, drawing primarily from studies of the lung, kidney, salivary gland, mammary gland, and pancreas, all of which contain epithelial trees that form through collective cell behaviors. Much of our understanding of epithelial branching comes from experiments using mice, but we also include examples here from avian and reptilian models. Throughout, we highlight how distinct mechanisms are employed in different organs and species to build epithelial trees. We also highlight how similar morphogenetic motifs are used to carry out conserved developmental programs or repurposed to support novel ones. Understanding the unique strategies used by nature to build branched epithelia from across the tree of life can help to inspire creative solutions to problems in tissue engineering and regenerative medicine.
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21
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Genomic, transcriptomic, and epigenomic analysis of a medicinal snake, Bungarus multicinctus, to provides insights into the origin of Elapidae neurotoxins. Acta Pharm Sin B 2022; 13:2234-2249. [DOI: 10.1016/j.apsb.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/20/2022] [Accepted: 11/11/2022] [Indexed: 11/19/2022] Open
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22
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van Ineveld RL, Collot R, Román MB, Pagliaro A, Bessler N, Ariese HCR, Kleinnijenhuis M, Kool M, Alieva M, Chuva de Sousa Lopes SM, Wehrens EJ, Rios AC. Multispectral confocal 3D imaging of intact healthy and tumor tissue using mLSR-3D. Nat Protoc 2022; 17:3028-3055. [PMID: 36180532 DOI: 10.1038/s41596-022-00739-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 06/16/2022] [Indexed: 11/09/2022]
Abstract
Revealing the 3D composition of intact tissue specimens is essential for understanding cell and organ biology in health and disease. State-of-the-art 3D microscopy techniques aim to capture tissue volumes on an ever-increasing scale, while also retaining sufficient resolution for single-cell analysis. Furthermore, spatial profiling through multi-marker imaging is fast developing, providing more context and better distinction between cell types. Following these lines of technological advance, we here present a protocol based on FUnGI (fructose, urea and glycerol clearing solution for imaging) optical clearing of tissue before multispectral large-scale single-cell resolution 3D (mLSR-3D) imaging, which implements 'on-the-fly' linear unmixing of up to eight fluorophores during a single acquisition. Our protocol removes the need for repetitive illumination, thereby allowing larger volumes to be scanned with better image quality in less time, also reducing photo-bleaching and file size. To aid in the design of multiplex antibody panels, we provide a fast and manageable intensity equalization assay with automated analysis to design a combination of markers with balanced intensities suitable for mLSR-3D. We demonstrate effective mLSR-3D imaging of various tissues, including patient-derived organoids and xenografted tumors, and, furthermore, describe an optimized workflow for mLSR-3D imaging of formalin-fixed paraffin-embedded samples. Finally, we provide essential steps for 3D image data processing, including shading correction that does not require pre-acquired shading references and 3D inhomogeneity correction to correct fluorescence artefacts often afflicting 3D datasets. Together, this provides a one-week protocol for eight-fluorescent-marker 3D visualization and exploration of intact tissue of various origins at single-cell resolution.
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Affiliation(s)
- Ravian L van Ineveld
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Raphaël Collot
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Mario Barrera Román
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Anna Pagliaro
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Nils Bessler
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Hendrikus C R Ariese
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Michiel Kleinnijenhuis
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Marcel Kool
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center DKFZ and German Cancer Consortium DKTK, Heidelberg, Germany
| | - Maria Alieva
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | | | - Ellen J Wehrens
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands. .,Oncode Institute, Utrecht, the Netherlands.
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23
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Venom Variation of Neonate and Adult Chinese Cobras in Captivity Concerning Their Foraging Strategies. Toxins (Basel) 2022; 14:toxins14090598. [PMID: 36136536 PMCID: PMC9501182 DOI: 10.3390/toxins14090598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/18/2022] [Accepted: 08/26/2022] [Indexed: 11/22/2022] Open
Abstract
The venom and transcriptome profile of the captive Chinese cobra (Naja atra) is not characterized until now. Here, LC-MS/MS and illumine technology were used to unveil the venom and trascriptome of neonates and adults N. atra specimens. In captive Chinese cobra, 98 co-existing transcripts for venom-related proteins was contained. A total of 127 proteins belong to 21 protein families were found in the profile of venom. The main components of snake venom were three finger toxins (3-FTx), snake venom metalloproteinase (SVMP), cysteine-rich secretory protein (CRISP), cobra venom factor (CVF), and phosphodiesterase (PDE). During the ontogenesis of captive Chinese cobra, the rearrangement of snake venom composition occurred and with obscure gender difference. CVF, 3-FTx, PDE, phospholipase A2 (PLA2) in adults were more abundant than neonates, while SVMP and CRISP in the neonates was richer than the adults. Ontogenetic changes in the proteome of Chinese cobra venom reveals different strategies for handling prey. The levels of different types of toxin families were dramatically altered in the wild and captive specimens. Therefore, we speculate that the captive process could reshape the snake venom composition vigorously. The clear comprehension of the composition of Chinese cobra venom facilitates the understanding of the mechanism of snakebite intoxication and guides the preparation and administration of traditional antivenom and next-generation drugs for snakebite.
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24
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Lin W, Lu X, Yang H, Huang L, Huang W, Tang Y, Liu S, Wang H, Zhang Y. Metabolic heterogeneity protects metastatic mucosal melanomas cells from ferroptosis. Int J Mol Med 2022; 50:124. [PMID: 36004461 PMCID: PMC9448297 DOI: 10.3892/ijmm.2022.5180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/18/2022] [Indexed: 11/08/2022] Open
Abstract
Cancer heterogeneity has been proposed to be one of the main causes of metastatic dissemination and therapy failure. However, the underlying mechanisms of this phenomenon remain poorly understood. Melanoma is an aggressive malignancy with a high heterogeneity and metastatic potential. Therefore, the present study investigated the possible association between cancer heterogeneity and metastasis in melanoma. In total, two novel Chinese oral mucosal melanoma (COMM) cell lines, namely COMM-1 and COMM-2, were established for exploring methods into preventing the loss of cellular heterogeneity caused by long-term cell culture. Each cell line was grown under two different models of culture, which yielded two subtypes, one exhibited an adhesive morphology (COMM-AD), whereas the other was grown in suspension (COMM-SUS). Compared with the COMM-AD cells, the COMM-SUS cells exhibited higher metastatic capacities and autofluorescence. Further investigations indicated that the COMM-SUS cells exhibited metabolic reprogramming by taking up lactate produced by COMM-AD cells at increased levels to accumulate NADH through monocarboxylate transporter 1, whilst also increasing NADPH levels through the pentose phosphate pathway (PPP). Additionally, increased NADH and NADPH levels in the COMM-SUS cells, coupled with the upregulation of the anti-ferroptotic proteins, glutathione peroxidase 4 and ferroptosis suppressor protein 1, enabled them to resist ferroptotic cell death induced by oxidative stress during hematogenous dissemination. The inhibition of ferroptosis was found to substantially increase the metastatic capacity of COMM-AD cells. Furthermore, suppressing lactate uptake and impairing PPP activation significantly decreased the metastatic potential of the COMM-SUS cells. Thus, the present study on metabolic heterogeneity in COMM cells potentially provides a novel perspective for exploring this mechanism underlying cancer metastasis.
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Affiliation(s)
- Weifan Lin
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat‑sen University, Guangzhou, Guangdong 510006, P.R. China
| | - Xiangwan Lu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat‑sen University, Guangzhou, Guangdong 510006, P.R. China
| | - Hang Yang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat‑sen University, Guangzhou, Guangdong 510006, P.R. China
| | - Linxuan Huang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat‑sen University, Guangzhou, Guangdong 510006, P.R. China
| | - Wuheng Huang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat‑sen University, Guangzhou, Guangdong 510006, P.R. China
| | - Yuluan Tang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat‑sen University, Guangzhou, Guangdong 510006, P.R. China
| | - Situn Liu
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat‑sen University, Guangzhou, Guangdong 510006, P.R. China
| | - Hua Wang
- Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Guanghua Hospital of Stomatology, Sun Yat‑sen University, Guangzhou, Guangdong 510055, P.R. China
| | - Yan Zhang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat‑sen University, Guangzhou, Guangdong 510006, P.R. China
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25
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Physiological constraints dictate toxin spatial heterogeneity in snake venom glands. BMC Biol 2022; 20:148. [PMID: 35761243 PMCID: PMC9238143 DOI: 10.1186/s12915-022-01350-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/13/2022] [Indexed: 11/20/2022] Open
Abstract
Background Venoms are ecological innovations that have evolved numerous times, on each occasion accompanied by the co-evolution of specialised morphological and behavioural characters for venom production and delivery. The close evolutionary interdependence between these characters is exemplified by animals that control the composition of their secreted venom. This ability depends in part on the production of different toxins in different locations of the venom gland, which was recently documented in venomous snakes. Here, we test the hypothesis that the distinct spatial distributions of toxins in snake venom glands are an adaptation that enables the secretion of venoms with distinct ecological functions. Results We show that the main defensive and predatory peptide toxins are produced in distinct regions of the venom glands of the black-necked spitting cobra (Naja nigricollis), but these distributions likely reflect developmental effects. Indeed, we detected no significant differences in venom collected via defensive ‘spitting’ or predatory ‘biting’ events from the same specimens representing multiple lineages of spitting cobra. We also found the same spatial distribution of toxins in a non-spitting cobra and show that heterogeneous toxin distribution is a feature shared with a viper with primarily predatory venom. Conclusions Our findings suggest that heterogeneous distributions of toxins are not an adaptation to controlling venom composition in snakes. Instead, it likely reflects physiological constraints on toxin production by the venom glands, opening avenues for future research on the mechanisms of functional differentiation of populations of protein-secreting cells within adaptive contexts. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01350-y.
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26
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Perry BW, Gopalan SS, Pasquesi GIM, Schield DR, Westfall AK, Smith CF, Koludarov I, Chippindale PT, Pellegrino MW, Chuong EB, Mackessy SP, Castoe TA. Snake venom gene expression is coordinated by novel regulatory architecture and the integration of multiple co-opted vertebrate pathways. Genome Res 2022; 32:1058-1073. [PMID: 35649579 PMCID: PMC9248877 DOI: 10.1101/gr.276251.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 04/11/2022] [Indexed: 11/25/2022]
Abstract
Understanding how regulatory mechanisms evolve is critical for understanding the processes that give rise to novel phenotypes. Snake venom systems represent a valuable and tractable model for testing hypotheses related to the evolution of novel regulatory networks, yet the regulatory mechanisms underlying venom production remain poorly understood. Here, we use functional genomics approaches to investigate venom regulatory architecture in the prairie rattlesnake and identify cis-regulatory sequences (enhancers and promoters), trans-regulatory transcription factors, and integrated signaling cascades involved in the regulation of snake venom genes. We find evidence that two conserved vertebrate pathways, the extracellular signal-regulated kinase and unfolded protein response pathways, were co-opted to regulate snake venom. In one large venom gene family (snake venom serine proteases), this co-option was likely facilitated by the activity of transposable elements. Patterns of snake venom gene enhancer conservation, in some cases spanning 50 million yr of lineage divergence, highlight early origins and subsequent lineage-specific adaptations that have accompanied the evolution of venom regulatory architecture. We also identify features of chromatin structure involved in venom regulation, including topologically associated domains and CTCF loops that underscore the potential importance of novel chromatin structure to coevolve when duplicated genes evolve new regulatory control. Our findings provide a model for understanding how novel regulatory systems may evolve through a combination of genomic processes, including tandem duplication of genes and regulatory sequences, cis-regulatory sequence seeding by transposable elements, and diverse transcriptional regulatory proteins controlled by a co-opted regulatory cascade.
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Affiliation(s)
- Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA.,School of Biological Sciences, Washington State University, Pullman, Washington 99164, USA
| | - Siddharth S Gopalan
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Giulia I M Pasquesi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Drew R Schield
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Aundrea K Westfall
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Cara F Smith
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado 80639, USA
| | - Ivan Koludarov
- Animal Venomics Group, Justus Liebig University, Giessen, 35390, Germany
| | - Paul T Chippindale
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Mark W Pellegrino
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Edward B Chuong
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado 80639, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
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27
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von Reumont BM, Anderluh G, Antunes A, Ayvazyan N, Beis D, Caliskan F, Crnković A, Damm M, Dutertre S, Ellgaard L, Gajski G, German H, Halassy B, Hempel BF, Hucho T, Igci N, Ikonomopoulou MP, Karbat I, Klapa MI, Koludarov I, Kool J, Lüddecke T, Ben Mansour R, Vittoria Modica M, Moran Y, Nalbantsoy A, Ibáñez MEP, Panagiotopoulos A, Reuveny E, Céspedes JS, Sombke A, Surm JM, Undheim EAB, Verdes A, Zancolli G. Modern venomics-Current insights, novel methods, and future perspectives in biological and applied animal venom research. Gigascience 2022; 11:6588117. [PMID: 35640874 PMCID: PMC9155608 DOI: 10.1093/gigascience/giac048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 12/11/2022] Open
Abstract
Venoms have evolved >100 times in all major animal groups, and their components, known as toxins, have been fine-tuned over millions of years into highly effective biochemical weapons. There are many outstanding questions on the evolution of toxin arsenals, such as how venom genes originate, how venom contributes to the fitness of venomous species, and which modifications at the genomic, transcriptomic, and protein level drive their evolution. These questions have received particularly little attention outside of snakes, cone snails, spiders, and scorpions. Venom compounds have further become a source of inspiration for translational research using their diverse bioactivities for various applications. We highlight here recent advances and new strategies in modern venomics and discuss how recent technological innovations and multi-omic methods dramatically improve research on venomous animals. The study of genomes and their modifications through CRISPR and knockdown technologies will increase our understanding of how toxins evolve and which functions they have in the different ontogenetic stages during the development of venomous animals. Mass spectrometry imaging combined with spatial transcriptomics, in situ hybridization techniques, and modern computer tomography gives us further insights into the spatial distribution of toxins in the venom system and the function of the venom apparatus. All these evolutionary and biological insights contribute to more efficiently identify venom compounds, which can then be synthesized or produced in adapted expression systems to test their bioactivity. Finally, we critically discuss recent agrochemical, pharmaceutical, therapeutic, and diagnostic (so-called translational) aspects of venoms from which humans benefit.
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Affiliation(s)
- Bjoern M von Reumont
- Goethe University Frankfurt, Institute for Cell Biology and Neuroscience, Department for Applied Bioinformatics, 60438 Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Frankfurt, Senckenberganlage 25, 60235 Frankfurt, Germany.,Justus Liebig University Giessen, Institute for Insectbiotechnology, Heinrich Buff Ring 26-32, 35396 Giessen, Germany
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Naira Ayvazyan
- Orbeli Institute of Physiology of NAS RA, Orbeli ave. 22, 0028 Yerevan, Armenia
| | - Dimitris Beis
- Developmental Biology, Centre for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens 11527, Greece
| | - Figen Caliskan
- Department of Biology, Faculty of Science and Letters, Eskisehir Osmangazi University, TR-26040 Eskisehir, Turkey
| | - Ana Crnković
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Maik Damm
- Technische Universität Berlin, Department of Chemistry, Straße des 17. Juni 135, 10623 Berlin, Germany
| | | | - Lars Ellgaard
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Goran Gajski
- Institute for Medical Research and Occupational Health, Mutagenesis Unit, Ksaverska cesta 2, 10000 Zagreb, Croatia
| | - Hannah German
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
| | - Beata Halassy
- University of Zagreb, Centre for Research and Knowledge Transfer in Biotechnology, Trg Republike Hrvatske 14, 10000 Zagreb, Croatia
| | - Benjamin-Florian Hempel
- BIH Center for Regenerative Therapies BCRT, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Tim Hucho
- Translational Pain Research, Department of Anesthesiology and Intensive Care Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Nasit Igci
- Nevsehir Haci Bektas Veli University, Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, 50300 Nevsehir, Turkey
| | - Maria P Ikonomopoulou
- Madrid Institute for Advanced Studies in Food, Madrid,E28049, Spain.,The University of Queensland, St Lucia, QLD 4072, Australia
| | - Izhar Karbat
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Maria I Klapa
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology Hellas (FORTH/ICE-HT), Patras GR-26504, Greece
| | - Ivan Koludarov
- Justus Liebig University Giessen, Institute for Insectbiotechnology, Heinrich Buff Ring 26-32, 35396 Giessen, Germany
| | - Jeroen Kool
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
| | - Tim Lüddecke
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Frankfurt, Senckenberganlage 25, 60235 Frankfurt, Germany.,Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, 35392 Gießen, Germany
| | - Riadh Ben Mansour
- Department of Life Sciences, Faculty of Sciences, Gafsa University, Campus Universitaire Siidi Ahmed Zarrouk, 2112 Gafsa, Tunisia
| | - Maria Vittoria Modica
- Dept. of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Via Po 25c, I-00198 Roma, Italy
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ayse Nalbantsoy
- Department of Bioengineering, Faculty of Engineering, Ege University, 35100 Bornova, Izmir, Turkey
| | - María Eugenia Pachón Ibáñez
- Unit of Infectious Diseases, Microbiology, and Preventive Medicine, Virgen del Rocío University Hospital, Institute of Biomedicine of Seville, 41013 Sevilla, Spain.,CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Alexios Panagiotopoulos
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology Hellas (FORTH/ICE-HT), Patras GR-26504, Greece.,Animal Biology Division, Department of Biology, University of Patras, Patras, GR-26500, Greece
| | - Eitan Reuveny
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Javier Sánchez Céspedes
- Unit of Infectious Diseases, Microbiology, and Preventive Medicine, Virgen del Rocío University Hospital, Institute of Biomedicine of Seville, 41013 Sevilla, Spain.,CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Andy Sombke
- Department of Evolutionary Biology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Joachim M Surm
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Eivind A B Undheim
- University of Oslo, Centre for Ecological and Evolutionary Synthesis, Postboks 1066 Blindern 0316 Oslo, Norway
| | - Aida Verdes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Giulia Zancolli
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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28
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Ineveld RL, Vliet EJ, Wehrens EJ, Alieva M, Rios AC. 3D imaging for driving cancer discovery. EMBO J 2022; 41:e109675. [PMID: 35403737 PMCID: PMC9108604 DOI: 10.15252/embj.2021109675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/09/2022] [Accepted: 03/09/2022] [Indexed: 11/09/2022] Open
Abstract
Our understanding of the cellular composition and architecture of cancer has primarily advanced using 2D models and thin slice samples. This has granted spatial information on fundamental cancer biology and treatment response. However, tissues contain a variety of interconnected cells with different functional states and shapes, and this complex organization is impossible to capture in a single plane. Furthermore, tumours have been shown to be highly heterogenous, requiring large-scale spatial analysis to reliably profile their cellular and structural composition. Volumetric imaging permits the visualization of intact biological samples, thereby revealing the spatio-phenotypic and dynamic traits of cancer. This review focuses on new insights into cancer biology uniquely brought to light by 3D imaging and concomitant progress in cancer modelling and quantitative analysis. 3D imaging has the potential to generate broad knowledge advance from major mechanisms of tumour progression to new strategies for cancer treatment and patient diagnosis. We discuss the expected future contributions of the newest imaging trends towards these goals and the challenges faced for reaching their full application in cancer research.
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Affiliation(s)
- Ravian L Ineveld
- Princess Máxima Center for Pediatric Oncology Utrecht The Netherlands
- Oncode Institute Utrecht The Netherlands
| | - Esmée J Vliet
- Princess Máxima Center for Pediatric Oncology Utrecht The Netherlands
- Oncode Institute Utrecht The Netherlands
| | - Ellen J Wehrens
- Princess Máxima Center for Pediatric Oncology Utrecht The Netherlands
- Oncode Institute Utrecht The Netherlands
| | - Maria Alieva
- Princess Máxima Center for Pediatric Oncology Utrecht The Netherlands
- Oncode Institute Utrecht The Netherlands
| | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology Utrecht The Netherlands
- Oncode Institute Utrecht The Netherlands
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29
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Abstract
The venom glands of reptiles, particularly those of front-fanged advanced snakes, must satisfy conflicting biological demands: rapid synthesis of potentially labile and highly toxic proteins, storage in the gland lumen for long periods, stabilization of the stored secretions, immediate activation of toxins upon deployment and protection of the animal from the toxic effects of its own venom. This dynamic system could serve as a model for the study of a variety of different phenomena involving exocrine gland activation, protein synthesis, stabilization of protein products and secretory mechanisms. However, these studies have been hampered by a lack of a long-term model that can be propagated in the lab (as opposed to whole-animal studies). Numerous attempts have been made to extend the lifetime of venom gland secretory cells, but only recently has an organoid model been shown to have the requisite qualities of recapitulation of the native system, self-propagation and long-term viability (>1 year). A tractable model is now available for myriad cell- and molecular-level studies of venom glands, protein synthesis and secretion. However, venom glands of reptiles are not identical, and many differ very extensively in overall architecture, microanatomy and protein products produced. This Review summarizes the similarities among and differences between venom glands of helodermatid lizards and of rear-fanged and front-fanged snakes, highlighting those areas that are well understood and identifying areas where future studies can fill in significant gaps in knowledge of these ancient, yet fascinating systems.
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Affiliation(s)
- Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, 501 20th St., CB 92, Greeley, CO 80639-0017, USA
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30
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Kim J, Koo BK, Clevers H. Organoid Studies in COVID-19 Research. Int J Stem Cells 2022; 15:3-13. [PMID: 35220288 PMCID: PMC8889327 DOI: 10.15283/ijsc21251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 01/15/2022] [Indexed: 01/08/2023] Open
Affiliation(s)
- Jihoon Kim
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, Korea
| | - Bon-Kyoung Koo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Korea
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, Netherlands
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31
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Rivera-de-Torre E, Rimbault C, Jenkins TP, Sørensen CV, Damsbo A, Saez NJ, Duhoo Y, Hackney CM, Ellgaard L, Laustsen AH. Strategies for Heterologous Expression, Synthesis, and Purification of Animal Venom Toxins. Front Bioeng Biotechnol 2022; 9:811905. [PMID: 35127675 PMCID: PMC8811309 DOI: 10.3389/fbioe.2021.811905] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/24/2021] [Indexed: 11/13/2022] Open
Abstract
Animal venoms are complex mixtures containing peptides and proteins known as toxins, which are responsible for the deleterious effect of envenomations. Across the animal Kingdom, toxin diversity is enormous, and the ability to understand the biochemical mechanisms governing toxicity is not only relevant for the development of better envenomation therapies, but also for exploiting toxin bioactivities for therapeutic or biotechnological purposes. Most of toxinology research has relied on obtaining the toxins from crude venoms; however, some toxins are difficult to obtain because the venomous animal is endangered, does not thrive in captivity, produces only a small amount of venom, is difficult to milk, or only produces low amounts of the toxin of interest. Heterologous expression of toxins enables the production of sufficient amounts to unlock the biotechnological potential of these bioactive proteins. Moreover, heterologous expression ensures homogeneity, avoids cross-contamination with other venom components, and circumvents the use of crude venom. Heterologous expression is also not only restricted to natural toxins, but allows for the design of toxins with special properties or can take advantage of the increasing amount of transcriptomics and genomics data, enabling the expression of dormant toxin genes. The main challenge when producing toxins is obtaining properly folded proteins with a correct disulfide pattern that ensures the activity of the toxin of interest. This review presents the strategies that can be used to express toxins in bacteria, yeast, insect cells, or mammalian cells, as well as synthetic approaches that do not involve cells, such as cell-free biosynthesis and peptide synthesis. This is accompanied by an overview of the main advantages and drawbacks of these different systems for producing toxins, as well as a discussion of the biosafety considerations that need to be made when working with highly bioactive proteins.
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Affiliation(s)
- Esperanza Rivera-de-Torre
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- *Correspondence: Esperanza Rivera-de-Torre, ; Andreas H. Laustsen,
| | - Charlotte Rimbault
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Christoffer V. Sørensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anna Damsbo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Natalie J. Saez
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Yoan Duhoo
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Celeste Menuet Hackney
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Lars Ellgaard
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Andreas H. Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- *Correspondence: Esperanza Rivera-de-Torre, ; Andreas H. Laustsen,
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32
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Zancolli G, Reijnders M, Waterhouse RM, Robinson-Rechavi M. Convergent evolution of venom gland transcriptomes across Metazoa. Proc Natl Acad Sci U S A 2022; 119:e2111392119. [PMID: 34983844 PMCID: PMC8740685 DOI: 10.1073/pnas.2111392119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2021] [Indexed: 12/13/2022] Open
Abstract
Animals have repeatedly evolved specialized organs and anatomical structures to produce and deliver a mixture of potent bioactive molecules to subdue prey or predators-venom. This makes it one of the most widespread, convergent functions in the animal kingdom. Whether animals have adopted the same genetic toolkit to evolved venom systems is a fascinating question that still eludes us. Here, we performed a comparative analysis of venom gland transcriptomes from 20 venomous species spanning the main Metazoan lineages to test whether different animals have independently adopted similar molecular mechanisms to perform the same function. We found a strong convergence in gene expression profiles, with venom glands being more similar to each other than to any other tissue from the same species, and their differences closely mirroring the species phylogeny. Although venom glands secrete some of the fastest evolving molecules (toxins), their gene expression does not evolve faster than evolutionarily older tissues. We found 15 venom gland-specific gene modules enriched in endoplasmic reticulum stress and unfolded protein response pathways, indicating that animals have independently adopted stress response mechanisms to cope with mass production of toxins. This, in turn, activates regulatory networks for epithelial development, cell turnover, and maintenance, which seem composed of both convergent and lineage-specific factors, possibly reflecting the different developmental origins of venom glands. This study represents a first step toward an understanding of the molecular mechanisms underlying the repeated evolution of one of the most successful adaptive traits in the animal kingdom.
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Affiliation(s)
- Giulia Zancolli
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland;
- Evolutionary Bioinformatics Group, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Maarten Reijnders
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
- Evolutionary-Functional Genomics Group, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
- Evolutionary-Functional Genomics Group, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne 1015, Switzerland
- Evolutionary Bioinformatics Group, Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
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33
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Baudou FG, Rodriguez JP, Fusco L, de Roodt AR, De Marzi MC, Leiva L. South American snake venoms with abundant neurotoxic components. Composition and toxicological properties. A literature review. Acta Trop 2021; 224:106119. [PMID: 34481791 DOI: 10.1016/j.actatropica.2021.106119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 01/18/2023]
Abstract
In South America there are three snake genera with predominantly neurotoxic venoms: Crotalus, Micrurus and Hydrophis, which include nine species/subspecies, 97 species and a single marine species, respectively. Although accidents with neurotoxic venoms are less frequent than those with anticoagulant, cytotoxic or necrotic venoms (e.g. from Bothrops), they are of major public health importance. Venoms from genus Crotalus have been extensively studied, while data on the venoms from the other two genera are very limited, especially for Hydrophis. The venoms of North and South American Crotalus species show biochemical and physiopathological differences. The former species cause bothrops-like envenomation symptoms, while the latter mainly have neurotoxic and myotoxic effects, leading to respiratory paralysis and, occasionally, renal failure by myoglobinuria and death, often with no local lesions. Micrurus and Hydrophis also cause neurotoxic envenomations. Many studies have isolated, identified and characterized new enzymes and toxins, thus expanding the knowledge of snake venom composition. The present review summarizes the currently available information on neurotoxic venoms from South American snakes, with a focus on protein composition and toxicological properties. It also includes some comments concerning potential medical applications of elapid and crotalic toxins.
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Affiliation(s)
- Federico G Baudou
- Universidad Nacional de Luján (UNLu), Depto. de Ciencias Básicas, Luján, Buenos Aires, Argentina; Laboratorio de Inmunología, Instituto de Ecología y Desarrollo Sustentable (INEDES), UNLu-CONICET, Luján, Buenos Aires, Argentina.
| | - Juan P Rodriguez
- Laboratorio de Investigaciones Bioquímicas de la Facultad de Medicina (LIBIM), Instituto de Química Básica y Aplicada del Nordeste Argentino (IQUIBA-NEA), Universidad Nacional del Nordeste, Consejo Nacional de Investigaciones Científicas y Técnicas (UNNE-CONICET), Corrientes, Argentina
| | - Luciano Fusco
- Laboratorio de Investigación en Proteínas (LabInPro), IQUIBA-NEA (UNNE, CONICET), FaCENA, (UNNE), Corrientes, Argentina
| | - Adolfo R de Roodt
- Área Investigación y Desarrollo-Venenos, Instituto Nacional de Producción de Biológicos, Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán", Ministerio de Salud de la Nación, Argentina; Primera Cátedra de Toxicología, Facultad de Medicina, Universidad de Buenos Aires, Argentina; Laboratorio de Toxinopatología, Centro de Patología Experimental y Aplicada, Facultad de Medicina, Universidad de Buenos Aires, Argentina
| | - Mauricio C De Marzi
- Universidad Nacional de Luján (UNLu), Depto. de Ciencias Básicas, Luján, Buenos Aires, Argentina; Laboratorio de Inmunología, Instituto de Ecología y Desarrollo Sustentable (INEDES), UNLu-CONICET, Luján, Buenos Aires, Argentina
| | - Laura Leiva
- Laboratorio de Investigación en Proteínas (LabInPro), IQUIBA-NEA (UNNE, CONICET), FaCENA, (UNNE), Corrientes, Argentina
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34
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Vonk FJ, Bittenbinder MA, Kerkkamp HMI, Grashof DGB, Archer JP, Afonso S, Richardson MK, Kool J, van der Meijden A. A non-lethal method for studying scorpion venom gland transcriptomes, with a review of potentially suitable taxa to which it can be applied. PLoS One 2021; 16:e0258712. [PMID: 34793470 PMCID: PMC8601437 DOI: 10.1371/journal.pone.0258712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/05/2021] [Indexed: 12/24/2022] Open
Abstract
Scorpion venoms are mixtures of proteins, peptides and small molecular compounds with high specificity for ion channels and are therefore considered to be promising candidates in the venoms-to-drugs pipeline. Transcriptomes are important tools for studying the composition and expression of scorpion venom. Unfortunately, studying the venom gland transcriptome traditionally requires sacrificing the animal and therefore is always a single snapshot in time. This paper describes a new way of generating a scorpion venom gland transcriptome without sacrificing the animal, thereby allowing the study of the transcriptome at various time points within a single individual. By comparing these venom-derived transcriptomes to the traditional whole-telson transcriptomes we show that the relative expression levels of the major toxin classes are similar. We further performed a multi-day extraction using our proposed method to show the possibility of doing a multiple time point transcriptome analysis. This allows for the study of patterns of toxin gene activation over time a single individual, and allows assessment of the effects of diet, season and other factors that are known or likely to influence intraindividual venom composition. We discuss the gland characteristics that may allow this method to be successful in scorpions and provide a review of other venomous taxa to which this method may potentially be successfully applied.
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Affiliation(s)
- Freek J. Vonk
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Faculty of Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Animal Science and Health Cluster, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Mátyás A. Bittenbinder
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Faculty of Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Harald M. I. Kerkkamp
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Animal Science and Health Cluster, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | | | - John P. Archer
- CIBIO-InBIO, Biopolis, Universidade do Porto, Porto, Portugal
| | - Sandra Afonso
- CIBIO-InBIO, Biopolis, Universidade do Porto, Porto, Portugal
| | - Michael K. Richardson
- Animal Science and Health Cluster, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Jeroen Kool
- Faculty of Sciences, Division of BioAnalytical Chemistry, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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35
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Abstract
Organoids have complex three-dimensional structures that exhibit functionalities and feature architectures similar to those of in vivo organs and are developed from adult stem cells, embryonic stem cells, and pluripotent stem cells through a self-organization process. Organoids derived from adult epithelial stem cells are the most mature and extensive. In recent years, using organoid culture techniques, researchers have established various adult human tissue-derived epithelial organoids, including intestinal, colon, lung, liver, stomach, breast, and oral mucosal organoids, all of which exhibit strong research and application prospects. Studies have shown that epithelial organoids are mainly applied in drug discovery, personalized drug response testing, disease mechanism research, and regenerative medicine. In this review, we mainly discuss current organoid culture systems and potential applications of this technique with human epithelial tissue.
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Affiliation(s)
- Fengjiao Li
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Peng Zhang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China.,Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Hunan Normal University), Ministry of Education, College of Chemistry & Chemical Engineering, Changsha, Hunan 410081, China
| | - Saizhi Wu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Lianwen Yuan
- Department of Geriatric Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Zhonghua Liu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
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36
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Chen F, Qin M, Liu W, Wang F, Ren W, Xu H, Li F. Snake Venom Identification via Fluorescent Discrimination. Anal Chem 2021; 93:14025-14030. [PMID: 34528790 DOI: 10.1021/acs.analchem.1c02804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The identification and discrimination of snake venom are highly desired for timely clinical treatment. However, the complex components in snake venom make it a great challenge to achieve rapid and accurate identification. Inspired by the organism's taste sensing system, a fluorescent sensor array that could differentiate snake venoms was fabricated. The interaction of snake venoms with different fluorescent dyes in the sensor array gave rich information, based on which efficient detection of complex snake venom was achieved. The main six proteins of snake venom in the same concentration, different concentrations, and their mixtures were identified with 100% accuracy. Furthermore, seven snake venoms belonging to different snake families were discriminated in PBS buffer and human plasma. Interferents of bovine serum albumin (BSA), thrombin, and transferrin (TRF) demonstrated the practicability of the fluorescent sensor array. This strategy of a multiresponse sensor array provides an effective method for accurate and rapid venom toxicology analysis, benefiting early and timely clinical diagnosis and treatment.
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Affiliation(s)
- Fei Chen
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Guangdong Engineering & Technology Research Centre of Graphene-like Materials and Products, Jinan University, Guangzhou 510632, China
| | - Meng Qin
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, P. R. China
| | - Wei Liu
- College of Pharmacy, Xinxiang Medical University, Xinxiang 453000, China
| | - Fan Wang
- College of Pharmacy, Xinxiang Medical University, Xinxiang 453000, China
| | - Wanjie Ren
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Guangdong Engineering & Technology Research Centre of Graphene-like Materials and Products, Jinan University, Guangzhou 510632, China
| | - Huihua Xu
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Guangdong Engineering & Technology Research Centre of Graphene-like Materials and Products, Jinan University, Guangzhou 510632, China
| | - Fengyu Li
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Guangdong Engineering & Technology Research Centre of Graphene-like Materials and Products, Jinan University, Guangzhou 510632, China
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37
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Richardson MK. Theories, laws, and models in evo-devo. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 338:36-61. [PMID: 34570438 PMCID: PMC9292786 DOI: 10.1002/jez.b.23096] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/01/2021] [Accepted: 07/16/2021] [Indexed: 12/17/2022]
Abstract
Evolutionary developmental biology (evo‐devo) is the study of the evolution of developmental mechanisms. Here, I review some of the theories, models, and laws in evo‐devo, past and present. Nineteenth‐century evo‐devo was dominated by recapitulation theory and archetypes. It also gave us germ layer theory, the vertebral theory of the skull, floral organs as modified leaves, and the “inverted invertebrate” theory, among others. Newer theories and models include the frameshift theory, the genetic toolkit for development, the ABC model of flower development, the developmental hourglass, the zootype, Urbilateria, and the hox code. Some of these new theories show the influence of archetypes and recapitulation. Interestingly, recent studies support the old “primordial leaf,” “inverted invertebrate,” and “segmented head” theories. Furthermore, von Baer's first three laws may now need to be rehabilitated, and the hourglass model modified, in view of what Abzhanov has pointed out about the maternal‐zygotic transition. There are many supposed “laws” of evo‐devo but I argue that these are merely generalizations about trends in particular lineages. I argue that the “body plan” is an archetype, and is often used in such a way that it lacks any scientific meaning. Looking to the future, one challenge for evo‐devo will be to develop new theories and models to accommodate the wealth of new data from high‐throughput sequencing, including single‐cell sequencing. One step in this direction is the use of sophisticated in silico analyses, as in the “transcriptomic hourglass” models. Laws and other universal concepts, past and present, are reviewed. I show that many concepts focus on conserved aspects of development. The puzzle remains as to how embryonic phenotype, natural selection, and developmental mechanisms can be aligned to give an integrated view of evolution and development.
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Affiliation(s)
- Michael K Richardson
- Sylvius Laboratory, Institute of Biology, University of Leiden, Leiden, The Netherlands
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38
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Sang Y, Miller LC, Nelli RK, Giménez-Lirola LG. Harness Organoid Models for Virological Studies in Animals: A Cross-Species Perspective. Front Microbiol 2021; 12:725074. [PMID: 34603253 PMCID: PMC8481363 DOI: 10.3389/fmicb.2021.725074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/27/2021] [Indexed: 02/02/2023] Open
Abstract
Animal models and cell culture in vitro are primarily used in virus and antiviral immune research. Whereas the limitation of these models to recapitulate the viral pathogenesis in humans has been made well aware, it is imperative to introduce more efficient systems to validate emerging viruses in both domestic and wild animals. Organoids ascribe to representative miniatures of organs (i.e., mini-organs), which are derived from three-dimensional culture of stem cells under respective differential conditions mimicking endogenous organogenetic niches. Organoids have broadened virological studies in the human context, particularly in recent uses for COVID19 research. This review examines the status and potential for cross-species applied organotypic culture in validating emerging animal, particularly zoonotic, viruses in domestic and wild animals.
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Affiliation(s)
- Yongming Sang
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, United States
| | - Laura C Miller
- Virus and Prion Research Unit, National Animal Disease Center, United States Department of Agriculture, Agricultural Research Service, Ames, IA, United States
| | - Rahul K Nelli
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Luis Gabriel Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
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39
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Impact of Repetitive DNA Elements on Snake Genome Biology and Evolution. Cells 2021; 10:cells10071707. [PMID: 34359877 PMCID: PMC8303610 DOI: 10.3390/cells10071707] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 12/11/2022] Open
Abstract
The distinctive biology and unique evolutionary features of snakes make them fascinating model systems to elucidate how genomes evolve and how variation at the genomic level is interlinked with phenotypic-level evolution. Similar to other eukaryotic genomes, large proportions of snake genomes contain repetitive DNA, including transposable elements (TEs) and satellite repeats. The importance of repetitive DNA and its structural and functional role in the snake genome, remain unclear. This review highlights the major types of repeats and their proportions in snake genomes, reflecting the high diversity and composition of snake repeats. We present snakes as an emerging and important model system for the study of repetitive DNA under the impact of sex and microchromosome evolution. We assemble evidence to show that certain repetitive elements in snakes are transcriptionally active and demonstrate highly dynamic lineage-specific patterns as repeat sequences. We hypothesize that particular TEs can trigger different genomic mechanisms that might contribute to driving adaptive evolution in snakes. Finally, we review emerging approaches that may be used to study the expression of repetitive elements in complex genomes, such as snakes. The specific aspects presented here will stimulate further discussion on the role of genomic repeats in shaping snake evolution.
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40
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Calvete JJ, Lomonte B, Saviola AJ, Bonilla F, Sasa M, Williams DJ, Undheim EA, Sunagar K, Jackson TN. Mutual enlightenment: A toolbox of concepts and methods for integrating evolutionary and clinical toxinology via snake venomics and the contextual stance. Toxicon X 2021; 9-10:100070. [PMID: 34195606 PMCID: PMC8234350 DOI: 10.1016/j.toxcx.2021.100070] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 12/21/2022] Open
Abstract
Snakebite envenoming is a neglected tropical disease that may claim over 100,000 human lives annually worldwide. Snakebite occurs as the result of an interaction between a human and a snake that elicits either a defensive response from the snake or, more rarely, a feeding response as the result of mistaken identity. Snakebite envenoming is therefore a biological and, more specifically, an ecological problem. Snake venom itself is often described as a "cocktail", as it is a heterogenous mixture of molecules including the toxins (which are typically proteinaceous) responsible for the pathophysiological consequences of envenoming. The primary function of venom in snake ecology is pre-subjugation, with defensive deployment of the secretion typically considered a secondary function. The particular composition of any given venom cocktail is shaped by evolutionary forces that include phylogenetic constraints associated with the snake's lineage and adaptive responses to the snake's ecological context, including the taxa it preys upon and by which it is predated upon. In the present article, we describe how conceptual frameworks from ecology and evolutionary biology can enter into a mutually enlightening relationship with clinical toxinology by enabling the consideration of snakebite envenoming from an "ecological stance". We detail the insights that may emerge from such a perspective and highlight the ways in which the high-fidelity descriptive knowledge emerging from applications of -omics era technologies - "venomics" and "antivenomics" - can combine with evolutionary explanations to deliver a detailed understanding of this multifactorial health crisis.
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Affiliation(s)
- Juan J. Calvete
- Evolutionary and Translational Venomics Laboratory, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Bruno Lomonte
- Unidad de Proteómica, Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Anthony J. Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Fabián Bonilla
- Laboratorio de Investigación en Animales Peligrosos (LIAP), Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Mahmood Sasa
- Laboratorio de Investigación en Animales Peligrosos (LIAP), Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
- Museo de Zoología, Centro de Investigaciones en Biodiversidad y Ecología Tropical, Universidad de Costa Rica, Costa Rica
| | | | - Eivind A.B. Undheim
- Centre for Biodiversity Dynamics, Department of Biology, NTNU, Trondheim, Norway
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kartik Sunagar
- Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Timothy N.W. Jackson
- Australian Venom Research Unit, Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne, Australia
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41
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Buecker C, Merkle FT. Science shines in a new virtual SY-Stem. Development 2021; 148:269281. [PMID: 34170290 DOI: 10.1242/dev.188367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The third 'Symposium for the Next Generation of Stem Cell Research' (SY-Stem) was held virtually on 3-5 March 2021, having been cancelled in 2020 due to the COVID-19 pandemic. As in previous years, the meeting highlighted the work of early career researchers, ranging from postgraduate students to young group leaders working in developmental and stem cell biology. Here, we summarize the excellent work presented at the Symposium, which covered topics ranging from pluripotency, species-specific aspects of development and emerging technologies, through to organoids, single-cell technology and clinical applications.
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Affiliation(s)
- Christa Buecker
- Max Perutz Labs Vienna, University of Vienna, Vienna BioCenter, Dr Bohr Gasse 9, 1030 Vienna, Austria
| | - Florian T Merkle
- Metabolic Research Laboratories and Medical Research Council Metabolic Diseases Unit, Wellcome Trust - Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
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42
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Pardos-Blas JR, Irisarri I, Abalde S, Afonso CML, Tenorio MJ, Zardoya R. The genome of the venomous snail Lautoconus ventricosus sheds light on the origin of conotoxin diversity. Gigascience 2021; 10:giab037. [PMID: 34037232 PMCID: PMC8152183 DOI: 10.1093/gigascience/giab037] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/23/2021] [Accepted: 04/30/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Venoms are deadly weapons to subdue prey or deter predators that have evolved independently in many animal lineages. The genomes of venomous animals are essential to understand the evolutionary mechanisms involved in the origin and diversification of venoms. RESULTS Here, we report the chromosome-level genome of the venomous Mediterranean cone snail, Lautoconus ventricosus (Caenogastropoda: Conidae). The total size of the assembly is 3.59 Gb; it has high contiguity (N50 = 93.53 Mb) and 86.6 Mb of the genome assembled into the 35 largest scaffolds or pseudochromosomes. On the basis of venom gland transcriptomes, we annotated 262 complete genes encoding conotoxin precursors, hormones, and other venom-related proteins. These genes were scattered in the different pseudochromosomes and located within repetitive regions. The genes encoding conotoxin precursors were normally structured into 3 exons, which did not necessarily coincide with the 3 structural domains of the corresponding proteins. Additionally, we found evidence in the L. ventricosus genome for a past whole-genome duplication event by means of conserved gene synteny with the Pomacea canaliculata genome, the only one available at the chromosome level within Caenogastropoda. The whole-genome duplication event was further confirmed by the presence of a duplicated hox gene cluster. Key genes for gastropod biology including those encoding proteins related to development, shell formation, and sex were located in the genome. CONCLUSIONS The new high-quality L. ventricosus genome should become a reference for assembling and analyzing new gastropod genomes and will contribute to future evolutionary genomic studies among venomous animals.
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Affiliation(s)
- José Ramón Pardos-Blas
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Iker Irisarri
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, D-37077 Goettingen, Germany
- Campus Institute Data Science (CIDAS), Goettingen, Wilhelmsplatz 1, D-37073, Germany
| | - Samuel Abalde
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
- Department of Zoology, Swedish Museum of Natural History, Frescativägen 40, 11418 Stockholm, Sweden
| | - Carlos M L Afonso
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005–139 Faro, Portugal
| | - Manuel J Tenorio
- Departamento CMIM y Q. Inorgánica-INBIO, Facultad de Ciencias, Universidad de Cadiz, 11510 Puerto Real, Cádiz, Spain
| | - Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
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43
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Wood LD, Ewald AJ. Organoids in cancer research: a review for pathologist-scientists. J Pathol 2021; 254:395-404. [PMID: 33886125 DOI: 10.1002/path.5684] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/09/2021] [Accepted: 04/19/2021] [Indexed: 12/20/2022]
Abstract
The use of three-dimensional (3D) culture models for cancer research has expanded greatly in recent years, with studies in almost every tumor type addressing a wide variety of research questions. Multiple distinct 3D culture approaches are now available, each with its own advantages and disadvantages, as well as most effective applications. In this review, we focus on one of these 3D culture models, organoids, in which multicellular units are isolated from primary or metastatic tumors and cultured in extracellular matrix gels. Organoids can be studied in acute cultures for short times after isolation, or passaged and biobanked for long-term use. We define this model system and describe some key studies in which organoid culture models were used to investigate cellular strategies and molecular mechanisms driving cancer initiation and progression, highlighting research questions for which this model is particularly well suited. In addition, as interest in implementing organoid systems continues to expand, we discuss key considerations in developing a new organoid research program. Our goal is to demonstrate the power and utility of organoid models and provide guidance for investigators who are considering implementation of these models in their own research programs. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Laura D Wood
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew J Ewald
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.,Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
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44
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Logan JM, Beck A, Dunstan N, Allen L, Woods AE. Development of the venom delivery system in Elapidae snake species: Naja siamensis and Oxyuranus microlepidotus. Toxicon 2021; 199:12-19. [PMID: 34010665 DOI: 10.1016/j.toxicon.2021.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/07/2021] [Accepted: 05/03/2021] [Indexed: 11/16/2022]
Abstract
Many advanced snakes possess a unique venom delivery system which they utilise to subdue prey and for defence. Despite extensive efforts, the evolutionary differences in this key system between advanced snake families remains enigmatic. The current study has investigated the development of the venom delivery system using two oviparous Elapidae models, Naja siamensis and Oxyuranus microlepidotus. The development stages of the embryos in both models were detailed using previously standardised characterisation. Variations in the days post-oviposition between these stages was observed, despite a continuous development trajectory. These differences also translated to the development of the venom delivery system.
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Affiliation(s)
- Jessica M Logan
- Mechanisms in Cell Biology and Disease Research Group, Clinical and Health Sciences, University of South Australia, North Terrace, Adelaide, South Australia, 5001, Australia.
| | - Andrew Beck
- Clinical and Health Sciences, University of South Australia, North Terrace, Adelaide, South Australia, 5001, Australia.
| | - Nathan Dunstan
- Venom Supplies Pty Ltd., Tanunda, South Australia, Australia.
| | - Luke Allen
- Venom Supplies Pty Ltd., Tanunda, South Australia, Australia.
| | - Anthony E Woods
- Clinical and Health Sciences, University of South Australia, North Terrace, Adelaide, South Australia, 5001, Australia.
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45
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Simintiras CA, Dhakal P, Ranjit C, Fitzgerald HC, Balboula AZ, Spencer TE. Capture and metabolomic analysis of the human endometrial epithelial organoid secretome. Proc Natl Acad Sci U S A 2021; 118:e2026804118. [PMID: 33876774 PMCID: PMC8053979 DOI: 10.1073/pnas.2026804118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Suboptimal uterine fluid (UF) composition can lead to pregnancy loss and likely contributes to offspring susceptibility to chronic adult-onset disorders. However, our understanding of the biochemical composition and mechanisms underpinning UF formation and regulation remain elusive, particularly in humans. To address this challenge, we developed a high-throughput method for intraorganoid fluid (IOF) isolation from human endometrial epithelial organoids. The IOF is biochemically distinct to the extraorganoid fluid (EOF) and cell culture medium as evidenced by the exclusive presence of 17 metabolites in IOF. Similarly, 69 metabolites were unique to EOF, showing asymmetrical apical and basolateral secretion by the in vitro endometrial epithelium, in a manner resembling that observed in vivo. Contrasting the quantitative metabolomic profiles of IOF and EOF revealed donor-specific biochemical signatures of organoids. Subsequent RNA sequencing of these organoids from which IOF and EOF were derived established the capacity to readily perform organoid multiomics in tandem, and suggests that transcriptomic regulation underpins the observed secretory asymmetry. In summary, these data provided by modeling uterine luminal and basolateral fluid formation in vitro offer scope to better understand UF composition and regulation with potential impacts on female fertility and offspring well-being.
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Affiliation(s)
| | - Pramod Dhakal
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211
| | - Chaman Ranjit
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211
| | | | - Ahmed Z Balboula
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211
| | - Thomas E Spencer
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211;
- Department of Obstetrics, Gynecology, and Women's Health, University of Missouri, Columbia, MO 65201
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46
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Kretzschmar K. Cancer research using organoid technology. J Mol Med (Berl) 2021; 99:501-515. [PMID: 33057820 PMCID: PMC8026469 DOI: 10.1007/s00109-020-01990-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/14/2020] [Accepted: 10/05/2020] [Indexed: 12/12/2022]
Abstract
Organoid technology has rapidly transformed basic biomedical research and contributed to significant discoveries in the last decade. With the application of protocols to generate organoids from cancer tissue, organoid technology has opened up new opportunities for cancer research and therapy. Using organoid cultures derived from healthy tissues, different aspects of tumour initiation and progression are widely studied including the role of pathogens or specific cancer genes. Cancer organoid cultures, on the other hand, are applied to generate biobanks, perform drug screens, and study mutational signatures. With the incorporation of cellular components of the tumour microenvironment such as immune cells into the organoid cultures, the technology is now also exploited in the rapidly advancing field of immuno-oncology. In this review, I discuss how organoid technology is currently being utilised in cancer research and what obstacles are still to be overcome for its broader use in anti-cancer therapy.
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Affiliation(s)
- Kai Kretzschmar
- Mildred Scheel Early Career Centre (MSNZ) for Cancer Research Würzburg, University Hospital Würzburg, MSNZ/IZKF, Josef-Schneider-Str. 2, 97080, Würzburg, Germany.
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47
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Kishi Y, Parker J. Cell type innovation at the tips of the animal tree. Curr Opin Genet Dev 2021; 69:112-121. [PMID: 33784538 DOI: 10.1016/j.gde.2021.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/20/2021] [Accepted: 01/24/2021] [Indexed: 11/16/2022]
Abstract
Understanding how organs originate is challenging due to the twin problems of explaining how new cell types evolve and how collective interactions between cell types arise and become selectively advantageous. Animals are assemblages of organs and cell types of different antiquities, and among the most rapidly and convergently evolving are exocrine glands and their constituent secretory cell types. Such structures have arisen independently thousands of times across the Metazoa, impacting how animals chemically interact with their environments. The recurrent evolution of exocrine systems provides a paradigm for examining how qualitative phenotypic novelties arise from variation at the cellular level. Here, we take a hierarchical perspective, focusing on the evolutionary assembly of novel biosynthetic pathways and secretory cell types, and how both selection and non-adaptive molecular processes may combine to build the complex, modular architectures of many animal glands.
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Affiliation(s)
- Yuriko Kishi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, 91125, United States
| | - Joseph Parker
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, 91125, United States.
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48
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Gijzen L, Yousef Yengej FA, Schutgens F, Vormann MK, Ammerlaan CME, Nicolas A, Kurek D, Vulto P, Rookmaaker MB, Lanz HL, Verhaar MC, Clevers H. Culture and analysis of kidney tubuloids and perfused tubuloid cells-on-a-chip. Nat Protoc 2021; 16:2023-2050. [PMID: 33674788 DOI: 10.1038/s41596-020-00479-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 12/04/2020] [Indexed: 12/17/2022]
Abstract
Advanced in vitro kidney models are of great importance to the study of renal physiology and disease. Kidney tubuloids can be established from primary cells derived from adult kidney tissue or urine. Tubuloids are three-dimensional multicellular structures that recapitulate tubular function and have been used to study infectious, malignant, metabolic, and genetic diseases. For tubuloids to more closely represent the in vivo kidney, they can be integrated into an organ-on-a-chip system that has a more physiological tubular architecture and allows flow and interaction with vasculature or epithelial and mesenchymal cells from other organs. Here, we describe a detailed protocol for establishing tubuloid cultures from tissue and urine (1-3 weeks), as well as for generating and characterizing tubuloid cell-derived three-dimensional tubular structures in a perfused microfluidic multi-chip platform (7 d). The combination of the two systems yields a powerful in vitro tool that better recapitulates the complexity of the kidney tubule with donor-specific properties.
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Affiliation(s)
| | - Fjodor A Yousef Yengej
- Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, the Netherlands.,Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Frans Schutgens
- Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, the Netherlands.,Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Carola M E Ammerlaan
- Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, the Netherlands.,Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | | | | - Maarten B Rookmaaker
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Marianne C Verhaar
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, the Netherlands.
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49
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Holthaus D, Delgado-Betancourt E, Aebischer T, Seeber F, Klotz C. Harmonization of Protocols for Multi-Species Organoid Platforms to Study the Intestinal Biology of Toxoplasma gondii and Other Protozoan Infections. Front Cell Infect Microbiol 2021; 10:610368. [PMID: 33692963 PMCID: PMC7937733 DOI: 10.3389/fcimb.2020.610368] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/30/2020] [Indexed: 12/20/2022] Open
Abstract
The small intestinal epithelium is the primary route of infection for many protozoan parasites. Understanding the mechanisms of infection, however, has been hindered due to the lack of appropriate models that recapitulate the complexity of the intestinal epithelium. Here, we describe an in vitro platform using stem cell-derived intestinal organoids established for four species that are important hosts of Apicomplexa and other protozoa in a zoonotic context: human, mouse, pig and chicken. The focus was set to create organoid-derived monolayers (ODMs) using the transwell system amenable for infection studies, and we provide straightforward guidelines for their generation and differentiation from organ-derived intestinal crypts. To this end, we reduced medium variations to an absolute minimum, allowing generation and differentiation of three-dimensional organoids for all four species and the subsequent generation of ODMs. Quantitative RT-PCR, immunolabeling with antibodies against marker proteins as well as transepithelial-electrical resistance (TEER) measurements were used to characterize ODM's integrity and functional state. These experiments show an overall uniform generation of monolayers suitable for Toxoplasma gondii infection, although robustness in terms of generation of stable TEER levels and cell differentiation status varies from species to species. Murine duodenal ODMs were then infected with T. gondii and/or Giardia duodenalis, two parasites that temporarily co-inhabit the intestinal niche but have not been studied previously in cellular co-infection models. T. gondii alone did not alter TEER values, integrity and transcriptional abundance of tight junction components. In contrast, in G. duodenalis-infected ODMs all these parameters were altered and T. gondii had no apparent influence on the G. duodenalis-triggered phenotype. In conclusion, we provide robust protocols for the generation, differentiation and characterization of intestinal organoids and ODMs from four species. We show their applications for comparative studies on parasite-host interactions during the early phase of a T. gondii infection but also its use for co-infections with other relevant intestinal protozoans.
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Affiliation(s)
| | | | | | | | - Christian Klotz
- FG 16: Mycotic and Parasitic Agents and Mycobacteria, Robert Koch-Institute, Berlin, Germany
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50
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Fujii M, Sato T. Somatic cell-derived organoids as prototypes of human epithelial tissues and diseases. NATURE MATERIALS 2021; 20:156-169. [PMID: 32807924 DOI: 10.1038/s41563-020-0754-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/30/2020] [Indexed: 05/19/2023]
Abstract
Recent progress in our understanding of the regulation of epithelial tissue stem cells has allowed us to exploit their abilities and instruct them to self-organize into tissue-mimicking structures, so-called organoids. Organoids preserve the molecular, structural and functional characteristics of their tissues of origin, thus providing an attractive opportunity to study the biology of human tissues in health and disease. In parallel to deriving organoids from yet-uncultured epithelial tissues, the field is devoting a growing amount of effort to model human diseases using organoids. This Review describes multidisciplinary approaches for creating organoid models of human genetic, neoplastic, immunological and infectious diseases, and details how they have contributed to our understanding of disease biology. We further highlight the potential role as well as limitations of organoids in clinical practice and showcase the latest achievements and approaches for tuning the organoid culture system to position organoids in biologically defined settings and to grant organoids with better representation of human tissues.
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Affiliation(s)
- Masayuki Fujii
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan.
| | - Toshiro Sato
- Department of Organoid Medicine, Keio University School of Medicine, Tokyo, Japan.
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