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Navajas Acedo J. Complete persistence of the primary somatosensory system in zebrafish. Dev Biol 2024; 515:178-185. [PMID: 39021074 DOI: 10.1016/j.ydbio.2024.05.004] [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: 02/12/2024] [Revised: 03/20/2024] [Accepted: 05/07/2024] [Indexed: 07/20/2024]
Abstract
The somatosensory system detects peripheral stimuli that are translated into behaviors necessary for survival. Fishes and amphibians possess two somatosensory systems in the trunk: the primary somatosensory system, formed by the Rohon-Beard neurons, and the secondary somatosensory system, formed by the neural crest cell-derived neurons of the Dorsal Root Ganglia. Rohon-Beard neurons have been characterized as a transient population that mostly disappears during the first days of life and is functionally replaced by the Dorsal Root Ganglia. Here, I follow Rohon-Beard neurons in vivo and show that the entire repertoire remains present in zebrafish from 1-day post-fertilization until the juvenile stage, 15-days post-fertilization. These data indicate that zebrafish retain two complete somatosensory systems until at least a developmental stage when the animals display complex behavioral repertoires.
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Affiliation(s)
- Joaquín Navajas Acedo
- Biozentrum at University of Basel, Spitalstrasse 41, Basel, Switzerland; Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, WA, USA.
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2
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Karampelias C, Băloiu B, Rathkolb B, da Silva-Buttkus P, Bachar-Wikström E, Marschall S, Fuchs H, Gailus-Durner V, Chu L, Hrabě de Angelis M, Andersson O. Examining the liver-pancreas crosstalk reveals a role for the molybdenum cofactor in β-cell regeneration. Life Sci Alliance 2024; 7:e202402771. [PMID: 39159974 PMCID: PMC11333758 DOI: 10.26508/lsa.202402771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 08/07/2024] [Accepted: 08/08/2024] [Indexed: 08/21/2024] Open
Abstract
Regeneration of insulin-producing β-cells is an alternative avenue to manage diabetes, and it is crucial to unravel this process in vivo during physiological responses to the lack of β-cells. Here, we aimed to characterize how hepatocytes can contribute to β-cell regeneration, either directly or indirectly via secreted proteins or metabolites, in a zebrafish model of β-cell loss. Using lineage tracing, we show that hepatocytes do not directly convert into β-cells even under extreme β-cell ablation conditions. A transcriptomic analysis of isolated hepatocytes after β-cell ablation displayed altered lipid- and glucose-related processes. Based on the transcriptomics, we performed a genetic screen that uncovers a potential role of the molybdenum cofactor (Moco) biosynthetic pathway in β-cell regeneration and glucose metabolism in zebrafish. Consistently, molybdenum cofactor synthesis 2 (Mocs2) haploinsufficiency in mice indicated dysregulated glucose metabolism and liver function. Together, our study sheds light on the liver-pancreas crosstalk and suggests that the molybdenum cofactor biosynthesis pathway should be further studied in relation to glucose metabolism and diabetes.
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Affiliation(s)
- Christos Karampelias
- https://ror.org/056d84691 Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Institute of Diabetes and Regeneration Research, Helmholtz Munich, Neuherberg, Germany
| | - Bianca Băloiu
- https://ror.org/056d84691 Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Birgit Rathkolb
- https://ror.org/00cfam450 Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Patricia da Silva-Buttkus
- https://ror.org/00cfam450 Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany
| | - Etty Bachar-Wikström
- https://ror.org/056d84691 Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Susan Marschall
- https://ror.org/00cfam450 Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany
| | - Helmut Fuchs
- https://ror.org/00cfam450 Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany
| | - Valerie Gailus-Durner
- https://ror.org/00cfam450 Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany
| | - Lianhe Chu
- https://ror.org/056d84691 Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Hrabě de Angelis
- https://ror.org/00cfam450 Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Freising, Germany
| | - Olov Andersson
- https://ror.org/056d84691 Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
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3
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Ujiie H, Nishiya N, Yamamoto A, Takada T, Onodera M, Sasaki A, Oikawa T. Dexamethasone reduces cisplatin-induced hair cell damage by inducing cisplatin resistance through metallothionein-2. Cancer Chemother Pharmacol 2024:10.1007/s00280-024-04706-z. [PMID: 39141082 DOI: 10.1007/s00280-024-04706-z] [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: 03/26/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024]
Abstract
PURPOSE Hair cell damage is a common side effect caused by the anticancer drug cisplatin (CDDP), which reduces patient quality of life. One CDDP resistance mechanism that occurs in recurrent cancers is heavy metal detoxification by metallothionein-2 (mt2). Here, we show that in zebrafish larvae, dexamethasone (DEX) reduces CDDP-induced hair cell damage by enhancing mt2 expression. METHODS Transgenic zebrafish (cldn: gfp; atoh1: rfp) that express green and red fluorescent proteins in neuromasts and hair cells, respectively, were used. The zebrafish were pretreated with DEX at 52 h post-fertilization (hpf) for 8 h, followed by CDDP treatment for 12 h. The lateral line hair cells of CDDP-treated zebrafish at 72 hpf were observed by fluorescence microscopy. RESULTS Reporting odds ratio (ROR) analysis using an adverse event database indicated an association between a decrease in CDDP-induced ototoxicity and DEX as an antiemetic treatment for cancer chemotherapy. Pretreatment with DEX protected 72 hpf zebrafish hair cells from CDDP-induced damage. The expression of mt2 mRNA was significantly increased by the combination of 10 µM DEX with CDDP. Gene editing of mt2 reversed the protective effect of DEX against CDDP-induced damage in hair cells. CONCLUSION DEX protects hair cells from CDDP-induced damage through increased mt2 expression, which is a resistance mechanism for platinum-based anticancer drugs.
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Affiliation(s)
- Haruki Ujiie
- Department of Pharmacy, Iwate Medical University Hospital, 2-1-1 Idaidori, Yahaba-Cho, Iwate, Shiwa-gun, 028-3695, Japan
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba-Cho, Iwate, Shiwa-gun, 028-3694, Japan
| | - Naoyuki Nishiya
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba-Cho, Iwate, Shiwa-gun, 028-3694, Japan.
| | - Ami Yamamoto
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba-Cho, Iwate, Shiwa-gun, 028-3694, Japan
| | - Takeru Takada
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba-Cho, Iwate, Shiwa-gun, 028-3694, Japan
| | - Megumi Onodera
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba-Cho, Iwate, Shiwa-gun, 028-3694, Japan
| | - Ayana Sasaki
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba-Cho, Iwate, Shiwa-gun, 028-3694, Japan
| | - Takuya Oikawa
- Division of Integrated Information for Pharmaceutical Sciences, Department of Clinical Pharmacy, School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba-Cho, Iwate, Shiwa-gun, 028-3694, Japan
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4
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Rosen Y, Brbić M, Roohani Y, Swanson K, Li Z, Leskovec J. Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN. Nat Methods 2024; 21:1492-1500. [PMID: 38366243 PMCID: PMC11310084 DOI: 10.1038/s41592-024-02191-z] [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: 02/03/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint analysis of cross-species datasets to homologous genes. Here we present SATURN, a deep learning method for learning universal cell embeddings that encodes genes' biological properties using protein language models. By coupling protein embeddings from language models with RNA expression, SATURN integrates datasets profiled from different species regardless of their genomic similarity. SATURN can detect functionally related genes coexpressed across species, redefining differential expression for cross-species analysis. Applying SATURN to three species whole-organism atlases and frog and zebrafish embryogenesis datasets, we show that SATURN can effectively transfer annotations across species, even when they are evolutionarily remote. We also demonstrate that SATURN can be used to find potentially divergent gene functions between glaucoma-associated genes in humans and four other species.
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Affiliation(s)
- Yanay Rosen
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Maria Brbić
- School of Computer and Communication Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Yusuf Roohani
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Kyle Swanson
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Ziang Li
- Department of Computer Science and Technology, Tsinghua University, Beijing, China
| | - Jure Leskovec
- Department of Computer Science, Stanford University, Stanford, CA, USA.
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Romero A, Sanchez A, Jones JD, Ledesma K, El-Halawany MS, Hamouda AK, Bill BR. Optimization of Zebrafish Larvae 6-OHDA Exposure for Neurotoxin Induced Dopaminergic Marker Reduction. Zebrafish 2024; 21:287-293. [PMID: 38608227 DOI: 10.1089/zeb.2023.0098] [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] [Indexed: 04/14/2024] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder that is clinically assessed by motor symptoms associated with the loss of midbrain dopaminergic neurons affecting the quality of life for over 8.5 million people worldwide. The neurotoxin 6-hydroxydopamine (6-OHDA) has been used to chemically induce a PD-like state in zebrafish larvae by several laboratories; however, highly variable concentration, methodology, and reagents have resulted in conflicting results suggesting a need to investigate these issues of reproducibility. We propose a protocol that addresses the differences in methodology and induces changes in 6 days postfertilization (dpf) larvae utilizing a 24-h exposure at 3 dpf with 30 μM 6-OHDA. Despite ∼50% lethality, no morphological or development differences in surviving fish are observed. Definition of our model is defined by downregulation of the expression of th1 by reverse transcriptase-quantitative polymerase chain reaction, a marker for dopaminergic neurons and a reduction in movement. Additionally, we observed a downregulation of pink1 and an upregulation of sod1 and sod2, indicators of mitochondrial dysfunction and response to reactive oxygen species, respectively.
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Affiliation(s)
- Adrian Romero
- The University of Texas at Tyler College of Arts and Sciences Department of Biology, Tyler, Texas, USA
- The University of Texas Tyler Ben and Maytee Fisch College of Pharmacy, Tyler, Texas, USA
| | - Armando Sanchez
- The University of Texas at Tyler College of Arts and Sciences Department of Biology, Tyler, Texas, USA
| | - Jocelyn D Jones
- The University of Texas at Tyler College of Arts and Sciences Department of Biology, Tyler, Texas, USA
| | - Kristel Ledesma
- The University of Texas at Tyler College of Arts and Sciences Department of Biology, Tyler, Texas, USA
| | - Medhat S El-Halawany
- The University of Texas Tyler Ben and Maytee Fisch College of Pharmacy, Tyler, Texas, USA
| | - Ayman K Hamouda
- The University of Texas Tyler Ben and Maytee Fisch College of Pharmacy, Tyler, Texas, USA
| | - Brent R Bill
- The University of Texas at Tyler College of Arts and Sciences Department of Biology, Tyler, Texas, USA
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Sun K, Liu X, Xu R, Liu C, Meng A, Lan X. Mapping the chromatin accessibility landscape of zebrafish embryogenesis at single-cell resolution by SPATAC-seq. Nat Cell Biol 2024; 26:1187-1199. [PMID: 38977847 DOI: 10.1038/s41556-024-01449-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/30/2024] [Indexed: 07/10/2024]
Abstract
Currently, the dynamic accessible elements that determine regulatory programs responsible for the unique identity and function of each cell type during zebrafish embryogenesis lack detailed study. Here we present SPATAC-seq: a split-pool ligation-based assay for transposase-accessible chromatin using sequencing. Using SPATAC-seq, we profiled chromatin accessibility in more than 800,000 individual nuclei across 20 developmental stages spanning the sphere stage to the early larval protruding mouth stage. Using this chromatin accessibility map, we identified 604 cell states and inferred their developmental relationships. We also identified 959,040 candidate cis-regulatory elements (cCREs) and delineated development-specific cCREs, as well as transcription factors defining diverse cell identities. Importantly, enhancer reporter assays confirmed that the majority of tested cCREs exhibited robust enhanced green fluorescent protein expression in restricted cell types or tissues. Finally, we explored gene regulatory programs that drive pigment and notochord cell differentiation. Our work provides a valuable open resource for exploring driver regulators of cell fate decisions in zebrafish embryogenesis.
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Affiliation(s)
- Keyong Sun
- School of Medicine, Tsinghua University, Beijing, China
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Tsinghua University, Beijing, China
| | - Xin Liu
- School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua University-Peking University Center for Life Sciences, Beijing, China
| | - Runda Xu
- School of Medicine, Tsinghua University, Beijing, China
- Tsinghua University-Peking University Center for Life Sciences, Beijing, China
| | - Chang Liu
- School of Medicine, Tsinghua University, Beijing, China
| | - Anming Meng
- School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua University-Peking University Center for Life Sciences, Beijing, China.
| | - Xun Lan
- School of Medicine, Tsinghua University, Beijing, China.
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Tsinghua University, Beijing, China.
- Tsinghua University-Peking University Center for Life Sciences, Beijing, China.
- Ministry of Education Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.
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7
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Dong Y, Lu R, Cao H, Zhang J, Wu X, Deng Y, Li JD. Deficiency in Prader-Willi syndrome gene necdin leads to attenuated cardiac contractility. iScience 2024; 27:109974. [PMID: 38832028 PMCID: PMC11144731 DOI: 10.1016/j.isci.2024.109974] [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: 09/25/2023] [Revised: 01/02/2024] [Accepted: 05/10/2024] [Indexed: 06/05/2024] Open
Abstract
Prader-Willi syndrome (PWS) is a genetic disorder characterized by behavioral disturbances, hyperphagia, and intellectual disability. Several surveys indicate that PWS is also associated with cardiac abnormalities, possibly contributing to a high incidence of sudden death. However, the pathological mechanisms underlying cardiac dysfunction in PWS remain unclear. In this study, we found that deficiency in necdin, an intronless gene within PWS region, led to heart systolic and diastolic dysfunction in mice. Through yeast two-hybrid screening, we identified an interaction between necdin and non-muscle myosin regulatory light chain 12a/b (MYL12 A/B). We further showed that necdin stabilized MYL12 A/B via SGT1-heat shock protein 90 (HSP90) chaperone machinery. The zebrafish lacking the MYL12 A/B analog, MYL12.1, exhibited impaired heart function, while cardiac-specific overexpression of MYL12A normalized the heart dysfunction in necdin-deficient mice. Our findings revealed necdin dysfunction as a contributing factor to cardiomyopathy in PWS patients and emphasized the importance of HSP90 chaperone machinery and non-muscle myosin in heart fitness.
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Affiliation(s)
- Yufan Dong
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, Hunan, P.R. China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha 410078, Hunan, P.R. China
| | - Renbin Lu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, Hunan, P.R. China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha 410078, Hunan, P.R. China
| | - Hui Cao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- Laboratory of Zebrafish Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Jing Zhang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, Hunan, P.R. China
- Hunan Key Laboratory of Animal Models for Human Diseases, Changsha 410078, Hunan, P.R. China
- Hunan Key Laboratory of Medical Genetics, Changsha 410078, Hunan, P.R. China
| | - Xiushan Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- Laboratory of Zebrafish Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yun Deng
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- Laboratory of Zebrafish Genetics, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Jia-Da Li
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, Hunan, P.R. China
- Hunan Key Laboratory of Animal Models for Human Diseases, Changsha 410078, Hunan, P.R. China
- Hunan Key Laboratory of Medical Genetics, Changsha 410078, Hunan, P.R. China
- Hunan International Scientific and Technological Cooperation Base of Animal Models for Human Diseases, Changsha 410078, Hunan, P.R. China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha 410078, Hunan, P.R. China
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Wilson ML, Romano SN, Khatri N, Aharon D, Liu Y, Kaufman OH, Draper BW, Marlow FL. Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component Mios. Nat Commun 2024; 15:5248. [PMID: 38898112 PMCID: PMC11187175 DOI: 10.1038/s41467-024-49613-2] [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: 01/25/2024] [Accepted: 06/12/2024] [Indexed: 06/21/2024] Open
Abstract
Reproductive success relies on proper establishment and maintenance of biological sex. In many animals, including mammals, the primary gonad is initially ovary biased. We previously showed the RNA binding protein (RNAbp), Rbpms2, is required for ovary fate in zebrafish. Here, we identified Rbpms2 targets in oocytes (Rbpms2-bound oocyte RNAs; rboRNAs). We identify Rbpms2 as a translational regulator of rboRNAs, which include testis factors and ribosome biogenesis factors. Further, genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway, specifically through the mTorc1-activating Gap activity towards Rags 2 (Gator2) component, Missing oocyte (Mios). Cumulatively, our findings indicate that early gonocytes are in a dual poised, bipotential state in which Rbpms2 acts as a binary fate-switch. Specifically, Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2-mediated checkpoint, thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis.
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Affiliation(s)
- Miranda L Wilson
- Department of Cell, Developmental, and Regenerative Biology. Icahn School of Medicine at Mount Sinai. One Gustave L. Levy Place Box 1020, New York, NY, USA
| | - Shannon N Romano
- Department of Cell, Developmental, and Regenerative Biology. Icahn School of Medicine at Mount Sinai. One Gustave L. Levy Place Box 1020, New York, NY, USA
| | - Nitya Khatri
- Department of Cell, Developmental, and Regenerative Biology. Icahn School of Medicine at Mount Sinai. One Gustave L. Levy Place Box 1020, New York, NY, USA
| | - Devora Aharon
- Department of Cell, Developmental, and Regenerative Biology. Icahn School of Medicine at Mount Sinai. One Gustave L. Levy Place Box 1020, New York, NY, USA
| | - Yulong Liu
- Department of Molecular and Cellular Biology. University of California. 1 Shields Ave, Davis, CA, USA
| | - Odelya H Kaufman
- Department of Developmental and Molecular Biology. Albert Einstein College of Medicine, Bronx, NY, USA
| | - Bruce W Draper
- Department of Molecular and Cellular Biology. University of California. 1 Shields Ave, Davis, CA, USA
| | - Florence L Marlow
- Department of Cell, Developmental, and Regenerative Biology. Icahn School of Medicine at Mount Sinai. One Gustave L. Levy Place Box 1020, New York, NY, USA.
- Department of Developmental and Molecular Biology. Albert Einstein College of Medicine, Bronx, NY, USA.
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9
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Liao XL, Chen ZF, Liu QY, Zhou JM, Cai WX, Wang Y, Cai Z. Tissue Accumulation and Biotransformation of 6PPD-Quinone in Adult Zebrafish and Its Effects on the Intestinal Microbial Community. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:10275-10286. [PMID: 38825773 DOI: 10.1021/acs.est.4c01409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The pronounced lethality of N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine quinone (6PPD-quinone or 6PPDQ) toward specific salmonids, while sparing other fish species, has received considerable attention. However, the underlying cause of this species-specific toxicity remains unresolved. This study explored 6PPDQ toxicokinetics and intestinal microbiota composition in adult zebrafish during a 14-day exposure to environmentally realistic concentrations, followed by a 7-day recovery phase. Predominant accumulation occurred in the brain, intestine, and eyes, with the lowest levels in the liver. Six metabolites were found to undergo hydroxylation, with two additionally undergoing O-sulfonation. Semiquantitative analyses revealed that the predominant metabolite featured a hydroxy group situated on the phenyl ring adjacent to the quinone. This was further validated by assessing enzyme activity and determining in silico binding interactions. Notably, the binding affinity between 6PPDQ and zebrafish phase I and II enzymes exceeded that with the corresponding coho salmon enzymes by 1.04-1.53 times, suggesting a higher potential for 6PPDQ detoxification in tolerant species. Whole-genome sequencing revealed significant increases in the genera Nocardioides and Rhodococcus after exposure to 6PPDQ. Functional annotation and pathway enrichment analyses predicted that these two genera would be responsible for the biodegradation and metabolism of xenobiotics. These findings offer crucial data for comprehending 6PPDQ-induced species-specific toxicity.
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Affiliation(s)
- Xiao-Liang Liao
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Zhi-Feng Chen
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Qian-Yi Liu
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Jia-Ming Zhou
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Wen-Xi Cai
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Yujie Wang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Zongwei Cai
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong 999077, China
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10
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Lalonde RL, Wells HH, Kemmler CL, Nieuwenhuize S, Lerma R, Burger A, Mosimann C. pIGLET: Safe harbor landing sites for reproducible and efficient transgenesis in zebrafish. SCIENCE ADVANCES 2024; 10:eadn6603. [PMID: 38838146 PMCID: PMC11152119 DOI: 10.1126/sciadv.adn6603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/03/2024] [Indexed: 06/07/2024]
Abstract
Standard zebrafish transgenesis involves random transgene integration with resource-intensive screening. While phiC31 integrase-based attP/attB recombination has streamlined transgenesis in mice and Drosophila, validated attP-based landing sites for universal applications are lacking in zebrafish. Here, we developed phiC31 Integrase Genomic Loci Engineered for Transgenesis (pIGLET) as transgenesis approach, with two attP landing sites pIGLET14a and pIGLET24b from well-validated Tol2 transgenes. Both sites facilitate diverse transgenesis applications including reporters and Cre/loxP transgenes. The pIGLET14a and pIGLET24b landing sites consistently yield 25 to 50% germline transmission, substantially reducing the resources needed for transgenic line generation. Transgenesis into these sites enables reproducible expression patterns in F0 zebrafish embryos for enhancer discovery and testing of gene regulatory variants. Together, our new landing sites streamline targeted, reproducible zebrafish transgenesis as a robust platform for various applications while minimizing the workload for generating transgenic lines.
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Affiliation(s)
| | | | - Cassie L. Kemmler
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Susan Nieuwenhuize
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Raymundo Lerma
- University of Colorado School of Medicine, Anschutz Medical Campus, Department of Pediatrics, Section of Developmental Biology, 12801 E 17th Avenue, Aurora, CO 80045, USA
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Isiaku AI, Zhang Z, Pazhakh V, Lieschke GJ. A nox2/cybb zebrafish mutant with defective myeloid cell reactive oxygen species production displays normal initial neutrophil recruitment to sterile tail injuries. G3 (BETHESDA, MD.) 2024; 14:jkae079. [PMID: 38696730 DOI: 10.1093/g3journal/jkae079] [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: 02/01/2024] [Accepted: 04/03/2024] [Indexed: 05/04/2024]
Abstract
Reactive oxygen species are important effectors and modifiers of the acute inflammatory response, recruiting phagocytes including neutrophils to sites of tissue injury. In turn, phagocytes such as neutrophils are both consumers and producers of reactive oxygen species. Phagocytes including neutrophils generate reactive oxygen species in an oxidative burst through the activity of a multimeric phagocytic nicotinamide adenine dinucleotide phosphate oxidase complex. Mutations in the NOX2/CYBB (previously gp91phox) nicotinamide adenine dinucleotide phosphate oxidase subunit are the commonest cause of chronic granulomatous disease, a disease characterized by infection susceptibility and an inflammatory phenotype. To model chronic granulomatous disease, we made a nox2/cybb zebrafish (Danio rerio) mutant and demonstrated it to have severely impaired myeloid cell reactive oxygen species production. Reduced early survival of nox2 mutant embryos indicated an essential requirement for nox2 during early development. In nox2/cybb zebrafish mutants, the dynamics of initial neutrophil recruitment to both mild and severe surgical tailfin wounds was normal, suggesting that excessive neutrophil recruitment at the initiation of inflammation is not the primary cause of the "sterile" inflammatory phenotype of chronic granulomatous disease patients. This nox2 zebrafish mutant adds to existing in vivo models for studying reactive oxygen species function in myeloid cells including neutrophils in development and disease.
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Affiliation(s)
- Abdulsalam I Isiaku
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Zuobing Zhang
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Vahid Pazhakh
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Graham J Lieschke
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
- Department of Clinical Haematology, Peter MacCallum Cancer Center and The Royal Melbourne Hospital, Parkville, VIC 3050, Australia
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12
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Baekelandt S, Leroux N, Lambert J, Bernay B, Robert JB, Burattin L, Gérard C, Delierneux C, Cornet V, Kestemont P. Evaluating the toxicity of estetrol, 17α-ethinylestradiol, and their combination with drospirenone on zebrafish larvae: A behavioural and proteomic study. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2024; 271:106941. [PMID: 38723469 DOI: 10.1016/j.aquatox.2024.106941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 04/29/2024] [Accepted: 05/04/2024] [Indexed: 05/21/2024]
Abstract
OBJECTIVE To characterise and compare the toxicity of estetrol (E4) and 17α-ethinylestradiol (EE2), and their respective mixture with the progestin drospirenone (DRSP) in zebrafish (Danio rerio) embryos. METHODS Zebrafish embryos were exposed to E4, EE2, DRSP, E4+DRSP, and EE2+DRSP in a fish embryo acute toxicity (FET) test. A second test examined behavioural responses and, using label-free proteomics, identified changes in protein expression in response to hormonal treatments, across a range of concentrations, including those that are considered to be environmentally relevant. RESULTS In the FET test, no effects were found from E4 at concentrations ≤100 mg/L, while EE2 induced mortality and morphological abnormalities at concentrations of 1-2 mg/L. In the behavioural test, exposure to 30 ng/L EE2 (∼200 × predicted environmental concentration - PEC) resulted in hypoactivity in fish larvae and exposure to 0.3 ng/L EE2 (∼2 × PEC) led to quantitative changes in protein abundance, revealing potential impacts on RNA processing and protein synthesis machinery. Exposure to E4 did not alter behaviour, but several groups of proteins were modulated, mainly at 710 ng/L (∼200 × PEC), including proteins involved in oxidative phosphorylation. When combined with DRSP, EE2 induced reduced effects on behaviour and proteomic responses, suggesting an antagonistic effect of DRSP. E4+DRSP induced no significant effects on behaviour or proteomic profiles at tested concentrations. CONCLUSIONS These findings suggest that E4-based combined oral contraceptives present a more favourable environmental profile than EE2-based contraceptives, particularly during the early developmental stages of fish.
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Affiliation(s)
- Sébastien Baekelandt
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth & Environment, University of Namur, Rue de Bruxelles 61, B-5000, Belgium.
| | - Nathalie Leroux
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth & Environment, University of Namur, Rue de Bruxelles 61, B-5000, Belgium
| | - Jérôme Lambert
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth & Environment, University of Namur, Rue de Bruxelles 61, B-5000, Belgium
| | - Benoît Bernay
- University of Caen Basse-Normandie, Proteogen Platform, SFR ICORE 4206, Esplanade de la Paix, Caen, CEDEX 14032, France
| | - Jean-Baptiste Robert
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth & Environment, University of Namur, Rue de Bruxelles 61, B-5000, Belgium
| | - Laura Burattin
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth & Environment, University of Namur, Rue de Bruxelles 61, B-5000, Belgium
| | - Céline Gérard
- Estetra SRL, an affiliate company of Mithra Pharmaceuticals, Rue Saint-Georges 5, Liège, 4000, Belgium
| | - Céline Delierneux
- Estetra SRL, an affiliate company of Mithra Pharmaceuticals, Rue Saint-Georges 5, Liège, 4000, Belgium
| | - Valérie Cornet
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth & Environment, University of Namur, Rue de Bruxelles 61, B-5000, Belgium
| | - Patrick Kestemont
- Research Unit in Environmental and Evolutionary Biology (URBE), Institute of Life, Earth & Environment, University of Namur, Rue de Bruxelles 61, B-5000, Belgium
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13
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Jacques F, Tichopád T, Demko M, Bystrý V, Křížová KC, Seifertová M, Voříšková K, Fuad MMH, Vetešník L, Šimková A. Reproduction-associated pathways in females of gibel carp (Carassius gibelio) shed light on the molecular mechanisms of the coexistence of asexual and sexual reproduction. BMC Genomics 2024; 25:548. [PMID: 38824502 PMCID: PMC11144346 DOI: 10.1186/s12864-024-10462-4] [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: 01/29/2024] [Accepted: 05/28/2024] [Indexed: 06/03/2024] Open
Abstract
Gibel carp (Carassius gibelio) is a cyprinid fish that originated in eastern Eurasia and is considered as invasive in European freshwater ecosystems. The populations of gibel carp in Europe are mostly composed of asexually reproducing triploid females (i.e., reproducing by gynogenesis) and sexually reproducing diploid females and males. Although some cases of coexisting sexual and asexual reproductive forms are known in vertebrates, the molecular mechanisms maintaining such coexistence are still in question. Both reproduction modes are supposed to exhibit evolutionary and ecological advantages and disadvantages. To better understand the coexistence of these two reproduction strategies, we performed transcriptome profile analysis of gonad tissues (ovaries) and studied the differentially expressed reproduction-associated genes in sexual and asexual females. We used high-throughput RNA sequencing to generate transcriptomic profiles of gonadal tissues of triploid asexual females and males, diploid sexual males and females of gibel carp, as well as diploid individuals from two closely-related species, C. auratus and Cyprinus carpio. Using SNP clustering, we showed the close similarity of C. gibelio and C. auratus with a basal position of C. carpio to both Carassius species. Using transcriptome profile analyses, we showed that many genes and pathways are involved in both gynogenetic and sexual reproduction in C. gibelio; however, we also found that 1500 genes, including 100 genes involved in cell cycle control, meiosis, oogenesis, embryogenesis, fertilization, steroid hormone signaling, and biosynthesis were differently expressed in the ovaries of asexual and sexual females. We suggest that the overall downregulation of reproduction-associated pathways in asexual females, and their maintenance in sexual ones, allows the populations of C. gibelio to combine the evolutionary and ecological advantages of the two reproductive strategies. However, we showed that many sexual-reproduction-related genes are maintained and expressed in asexual females, suggesting that gynogenetic gibel carp retains the genetic toolkits for meiosis and sexual reproduction. These findings shed new light on the evolution of this asexual and sexual complex.
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Affiliation(s)
- Florian Jacques
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic.
| | - Tomáš Tichopád
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics of the CAS, Liběchov, 277 21, Czech Republic
- Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, Vodňany, 389 25, Czech Republic
| | - Martin Demko
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Vojtěch Bystrý
- Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Kristína Civáňová Křížová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
| | - Mária Seifertová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
| | - Kristýna Voříšková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
| | - Md Mehedi Hasan Fuad
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
| | - Lukáš Vetešník
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
- Institute of Vertebrate Biology, Czech Academy of Science, Květná 8, Brno, 603 65, Czech Republic
| | - Andrea Šimková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
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14
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Hernandez-Huertas L, Moreno-Sanchez I, Crespo-Cuadrado J, Vargas-Baco A, da Silva Pescador G, Santos-Pereira JM, Bazzini AA, Moreno-Mateos MA. CRISPR-RfxCas13d screening uncovers Bckdk as a post-translational regulator of the maternal-to-zygotic transition in teleosts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595167. [PMID: 38826327 PMCID: PMC11142190 DOI: 10.1101/2024.05.22.595167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The Maternal-to-Zygotic transition (MZT) is a reprograming process encompassing zygotic genome activation (ZGA) and the clearance of maternally-provided mRNAs. While some factors regulating MZT have been identified, there are thousands of maternal RNAs whose function has not been ascribed yet. Here, we have performed a proof-of-principle CRISPR-RfxCas13d maternal screening targeting mRNAs encoding protein kinases and phosphatases in zebrafish and identified Bckdk as a novel post-translational regulator of MZT. Bckdk mRNA knockdown caused epiboly defects, ZGA deregulation, H3K27ac reduction and a partial impairment of miR-430 processing. Phospho-proteomic analysis revealed that Phf10/Baf45a, a chromatin remodeling factor, is less phosphorylated upon Bckdk depletion. Further, phf10 mRNA knockdown also altered ZGA and Phf10 constitutively phosphorylated rescued the developmental defects observed after bckdk mRNA depletion. Altogether, our results demonstrate the competence of CRISPR-RfxCas13d screenings to uncover new regulators of early vertebrate development and shed light on the post-translational control of MZT mediated by protein phosphorylation.
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Affiliation(s)
- Luis Hernandez-Huertas
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - Ismael Moreno-Sanchez
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - Jesús Crespo-Cuadrado
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - Ana Vargas-Baco
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain
| | | | - José M. Santos-Pereira
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
| | - Ariel A. Bazzini
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
| | - Miguel A. Moreno-Mateos
- Andalusian Center for Developmental Biology (CABD), Pablo de Olavide University/CSIC/Junta de Andalucía, Ctra. Utrera Km.1, 41013, Seville, Spain
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Ctra. Utrera Km.1, 41013, Seville, Spain
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15
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Baldarelli RM, Smith CL, Ringwald M, Richardson JE, Bult CJ. Mouse Genome Informatics: an integrated knowledgebase system for the laboratory mouse. Genetics 2024; 227:iyae031. [PMID: 38531069 PMCID: PMC11075557 DOI: 10.1093/genetics/iyae031] [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: 12/02/2023] [Accepted: 02/13/2024] [Indexed: 03/28/2024] Open
Abstract
Mouse Genome Informatics (MGI) is a federation of expertly curated information resources designed to support experimental and computational investigations into genetic and genomic aspects of human biology and disease using the laboratory mouse as a model system. The Mouse Genome Database (MGD) and the Gene Expression Database (GXD) are core MGI databases that share data and system architecture. MGI serves as the central community resource of integrated information about mouse genome features, variation, expression, gene function, phenotype, and human disease models acquired from peer-reviewed publications, author submissions, and major bioinformatics resources. To facilitate integration and standardization of data, biocuration scientists annotate using terms from controlled metadata vocabularies and biological ontologies (e.g. Mammalian Phenotype Ontology, Mouse Developmental Anatomy, Disease Ontology, Gene Ontology, etc.), and by applying international community standards for gene, allele, and mouse strain nomenclature. MGI serves basic scientists, translational researchers, and data scientists by providing access to FAIR-compliant data in both human-readable and compute-ready formats. The MGI resource is accessible at https://informatics.jax.org. Here, we present an overview of the core data types represented in MGI and highlight recent enhancements to the resource with a focus on new data and functionality for MGD and GXD.
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Affiliation(s)
| | | | | | | | - Carol J Bult
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
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16
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Wilson CA, Postlethwait JH. A maternal-to-zygotic-transition gene block on the zebrafish sex chromosome. G3 (BETHESDA, MD.) 2024; 14:jkae050. [PMID: 38466753 PMCID: PMC11075544 DOI: 10.1093/g3journal/jkae050] [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: 12/05/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/13/2024]
Abstract
Wild zebrafish (Danio rerio) have a ZZ/ZW chromosomal sex-determination system with the major sex locus on the right arm of chromosome-4 (Chr4R) near the largest heterochromatic block in the genome, suggesting that Chr4R transcriptomics might differ from the rest of the genome. To test this hypothesis, we conducted an RNA-seq analysis of adult ZW ovaries and ZZ testes in the Nadia strain and identified 4 regions of Chr4 with different gene expression profiles. Unique in the genome, protein-coding genes in a 41.7 Mb section (Region-2) were expressed in testis but silent in ovary. The AB lab strain, which lacks sex chromosomes, verified this result, showing that testis-biased gene expression in Region-2 depends on gonad biology, not on sex-determining mechanism. RNA-seq analyses in female and male brains and livers validated reduced transcripts from Region-2 in somatic cells, but without sex specificity. Region-2 corresponds to the heterochromatic portion of Chr4R and its content of genes and repetitive elements distinguishes it from the rest of the genome. Region-2 lacks protein-coding genes with human orthologs; has zinc finger genes expressed early in zygotic genome activation; has maternal 5S rRNA genes, maternal spliceosome genes, a concentration of tRNA genes, and a distinct set of repetitive elements. The colocalization of (1) genes silenced in ovaries but not in testes that are (2) expressed in embryos briefly at the onset of zygotic genome activation; (3) maternal-specific genes for translation machinery; (4) maternal-specific spliceosome components; and (5) adjacent genes encoding miR-430, which mediates maternal transcript degradation, suggest that this is a maternal-to-zygotic-transition gene regulatory block.
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17
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Schwartz AV, Sant KE, George UZ. danRerLib: a Python package for zebrafish transcriptomics. BIOINFORMATICS ADVANCES 2024; 4:vbae065. [PMID: 38770229 PMCID: PMC11105952 DOI: 10.1093/bioadv/vbae065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/12/2024] [Accepted: 05/03/2024] [Indexed: 05/22/2024]
Abstract
Summary Understanding the pathways and biological processes underlying differential gene expression is fundamental for characterizing gene expression changes in response to an experimental condition. Zebrafish, with a transcriptome closely mirroring that of humans, are frequently utilized as a model for human development and disease. However, a challenge arises due to the incomplete annotations of zebrafish pathways and biological processes, with more comprehensive annotations existing in humans. This incompleteness may result in biased functional enrichment findings and loss of knowledge. danRerLib, a versatile Python package for zebrafish transcriptomics researchers, overcomes this challenge and provides a suite of tools to be executed in Python including gene ID mapping, orthology mapping for the zebrafish and human taxonomy, and functional enrichment analysis utilizing the latest updated Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. danRerLib enables functional enrichment analysis for GO and KEGG pathways, even when they lack direct zebrafish annotations through the orthology of human-annotated functional annotations. This approach enables researchers to extend their analysis to a wider range of pathways, elucidating additional mechanisms of interest and greater insight into experimental results. Availability and implementation danRerLib, along with comprehensive documentation and tutorials, is freely available. The source code is available at https://github.com/sdsucomptox/danrerlib/ with associated documentation and tutorials at https://sdsucomptox.github.io/danrerlib/. The package has been developed with Python 3.9 and is available for installation on the package management systems PIP (https://pypi.org/project/danrerlib/) and Conda (https://anaconda.org/sdsu_comptox/danrerlib) with additional installation instructions on the documentation website.
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Affiliation(s)
- Ashley V Schwartz
- Computational Science Research Center, College of Sciences, San Diego State University, San Diego, CA 92182, United States
| | - Karilyn E Sant
- Computational Science Research Center, College of Sciences, San Diego State University, San Diego, CA 92182, United States
- Division of Environmental Health, School of Public Health, San Diego State University, San Diego, CA 92182, United States
| | - Uduak Z George
- Computational Science Research Center, College of Sciences, San Diego State University, San Diego, CA 92182, United States
- Department of Mathematics and Statistics, College of Sciences, San Diego State University, San Diego, CA 92182, United States
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18
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Pomreinke AP, Müller P. Zebrafish nampt-a mutants are viable despite perturbed primitive hematopoiesis. Hereditas 2024; 161:14. [PMID: 38685093 PMCID: PMC11057069 DOI: 10.1186/s41065-024-00318-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Nicotinamide phosphoribosyltransferase (Nampt) is required for recycling NAD+ in numerous cellular contexts. Morpholino-based knockdown of zebrafish nampt-a has been shown to cause abnormal development and defective hematopoiesis concomitant with decreased NAD+ levels. However, surprisingly, nampt-a mutant zebrafish were recently found to be viable, suggesting a discrepancy between the phenotypes in knockdown and knockout conditions. Here, we address this discrepancy by directly comparing loss-of-function approaches that result in identical defective transcripts in morphants and mutants. RESULTS Using CRISPR/Cas9-mediated mutagenesis, we generated nampt-a mutant lines that carry the same mis-spliced mRNA as nampt-a morphants. Despite reduced NAD+ levels and perturbed expression of specific blood markers, nampt-a mutants did not display obvious developmental defects and were found to be viable. In contrast, injection of nampt-a morpholinos into wild-type or mutant nampt-a embryos caused aberrant phenotypes. Moreover, nampt-a morpholinos caused additional reduction of blood-related markers in nampt-a mutants, suggesting that the defects observed in nampt-a morphants can be partially attributed to off-target effects of the morpholinos. CONCLUSIONS Our findings show that zebrafish nampt-a mutants are viable despite reduced NAD+ levels and a perturbed hematopoietic gene expression program, indicating strong robustness of primitive hematopoiesis during early embryogenesis.
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Affiliation(s)
- Autumn Penecilla Pomreinke
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
- University of Hohenheim, Stuttgart, Germany
| | - Patrick Müller
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany.
- University of Konstanz, Konstanz, Germany.
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19
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Muscò A, Martini D, Digregorio M, Broccoli V, Andreazzoli M. Shedding a Light on Dark Genes: A Comparative Expression Study of PRR12 Orthologues during Zebrafish Development. Genes (Basel) 2024; 15:492. [PMID: 38674426 PMCID: PMC11050278 DOI: 10.3390/genes15040492] [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: 03/16/2024] [Revised: 04/06/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Haploinsufficiency of the PRR12 gene is implicated in a human neuro-ocular syndrome. Although identified as a nuclear protein highly expressed in the embryonic mouse brain, PRR12 molecular function remains elusive. This study explores the spatio-temporal expression of zebrafish PRR12 co-orthologs, prr12a and prr12b, as a first step to elucidate their function. In silico analysis reveals high evolutionary conservation in the DNA-interacting domains for both orthologs, with significant syntenic conservation observed for the prr12b locus. In situ hybridization and RT-qPCR analyses on zebrafish embryos and larvae reveal distinct expression patterns: prr12a is expressed early in zygotic development, mainly in the central nervous system, while prr12b expression initiates during gastrulation, localizing later to dopaminergic telencephalic and diencephalic cell clusters. Both transcripts are enriched in the ganglion cell and inner neural layers of the 72 hpf retina, with prr12b widely distributed in the ciliary marginal zone. In the adult brain, prr12a and prr12b are found in the cerebellum, amygdala and ventral telencephalon, which represent the main areas affected in autistic patients. Overall, this study suggests PRR12's potential involvement in eye and brain development, laying the groundwork for further investigations into PRR12-related neurobehavioral disorders.
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Affiliation(s)
- Alessia Muscò
- Cell and Developmental Biology Unit, University of Pisa, 56126 Pisa, Italy (D.M.)
| | - Davide Martini
- Cell and Developmental Biology Unit, University of Pisa, 56126 Pisa, Italy (D.M.)
| | - Matteo Digregorio
- Cell and Developmental Biology Unit, University of Pisa, 56126 Pisa, Italy (D.M.)
| | - Vania Broccoli
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy
- CNR Institute of Neuroscience, 20132 Milan, Italy
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20
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Furukawa F, Aoyagi A, Sano K, Sameshima K, Goto M, Tseng YC, Ikeda D, Lin CC, Uchida K, Okumura SI, Yasumoto K, Jimbo M, Hwang PP. Gluconeogenesis in the extraembryonic yolk syncytial layer of the zebrafish embryo. PNAS NEXUS 2024; 3:pgae125. [PMID: 38585339 PMCID: PMC10997050 DOI: 10.1093/pnasnexus/pgae125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 03/11/2024] [Indexed: 04/09/2024]
Abstract
Yolk-consuming (lecithotrophic) embryos of oviparous animals, such as those of fish, need to make do with the maternally derived yolk. However, in many cases, yolk possesses little carbohydrates and sugars, including glucose, the essential monosaccharide. Interestingly, increases in the glucose content were found in embryos of some teleost fishes; however, the origin of this glucose has been unknown. Unveiling new metabolic strategies in fish embryos has a potential for better aquaculture technologies. In the present study, using zebrafish, we assessed how these embryos obtain the glucose. We employed stable isotope (13C)-labeled substrates and injected them to the zebrafish embryos. Our liquid chromatography-mass spectrometry-based isotope tracking revealed that among all tested substrate, glutamate was most actively metabolized to produce glucose in the zebrafish embryos. Expression analysis for gluconeogenic genes found that many of these were expressed in the yolk syncytial layer (YSL), an extraembryonic tissue found in teleost fishes. Generation 0 (G0) knockout of pck2, a gene encoding the key enzyme for gluconeogenesis from Krebs cycle intermediates, reduced gluconeogenesis from glutamate, suggesting that this gene is responsible for gluconeogenesis from glutamate in the zebrafish embryos. These results showed that teleost YSL undergoes gluconeogenesis, likely contributing to the glucose supplementation to the embryos with limited glucose source. Since many other animal lineages lack YSL, further comparative analysis will be interesting.
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Affiliation(s)
- Fumiya Furukawa
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Sec. 2, Nankang, Taipei 11529, Taiwan ROC
| | - Akihiro Aoyagi
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Kaori Sano
- Department of Chemistry, Faculty of Science, Josai University, 1-1 Keyakidai, Sakado, Saitama 350-0295, Japan
| | - Keita Sameshima
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Miku Goto
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Yung-Che Tseng
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Sec. 2, Nankang, Taipei 11529, Taiwan ROC
| | - Daisuke Ikeda
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Ching-Chun Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Sec. 2, Nankang, Taipei 11529, Taiwan ROC
| | - Katsuhisa Uchida
- Department of Marine Biology and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen Kibanadai-Nishi, Miyazaki 889-2192, Japan
| | - Sei-ichi Okumura
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Ko Yasumoto
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Mitsuru Jimbo
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Pung-Pung Hwang
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Sec. 2, Nankang, Taipei 11529, Taiwan ROC
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21
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Coppola U, Kenney J, Waxman JS. A Foxf1-Wnt-Nr2f1 cascade promotes atrial cardiomyocyte differentiation in zebrafish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584759. [PMID: 38558972 PMCID: PMC10980076 DOI: 10.1101/2024.03.13.584759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Nr2f transcription factors (TFs) are conserved regulators of vertebrate atrial cardiomyocyte (AC) differentiation. However, little is known about the mechanisms directing Nr2f expression in ACs. Here, we identified a conserved enhancer 3' to the nr2f1a locus, which we call 3'reg1-nr2f1a (3'reg1), that can promote Nr2f1a expression in ACs. Sequence analysis of the enhancer identified putative Lef/Tcf and Foxf TF binding sites. Mutation of the Lef/Tcf sites within the 3'reg1 reporter, knockdown of Tcf7l1a, and manipulation of canonical Wnt signaling support that Tcf7l1a is derepressed via Wnt signaling to activate the transgenic enhancer and promote AC differentiation. Similarly, mutation of the Foxf binding sites in the 3'reg1 reporter, coupled with gain- and loss-of-function analysis supported that Foxf1 promotes expression of the enhancer and AC differentiation. Functionally, we find that Wnt signaling acts downstream of Foxf1 to promote expression of the 3'reg1 reporter within ACs and, importantly, both Foxf1 and Wnt signaling require Nr2f1a to promote a surplus of differentiated ACs. CRISPR-mediated deletion of the endogenous 3'reg1 abrogates the ability of Foxf1 and Wnt signaling to produce surplus ACs in zebrafish embryos. Together, our data support that downstream members of a conserved regulatory network involving Wnt signaling and Foxf1 function on a nr2f1a enhancer to promote AC differentiation in the zebrafish heart.
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Affiliation(s)
- Ugo Coppola
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Jennifer Kenney
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Joshua S. Waxman
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Developmental Biology Division, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH 45229, USA
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22
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Wilson CA, Batzel P, Postlethwait JH. Direct male development in chromosomally ZZ zebrafish. Front Cell Dev Biol 2024; 12:1362228. [PMID: 38529407 PMCID: PMC10961373 DOI: 10.3389/fcell.2024.1362228] [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: 12/27/2023] [Accepted: 02/20/2024] [Indexed: 03/27/2024] Open
Abstract
The genetics of sex determination varies across taxa, sometimes even within a species. Major domesticated strains of zebrafish (Danio rerio), including AB and TU, lack a strong genetic sex determining locus, but strains more recently derived from nature, like Nadia (NA), possess a ZZ male/ZW female chromosomal sex-determination system. AB fish pass through a juvenile ovary stage, forming oocytes that survive in fish that become females but die in fish that become males. To understand mechanisms of gonad development in NA zebrafish, we studied histology and single cell transcriptomics in developing ZZ and ZW fish. ZW fish developed oocytes by 22 days post-fertilization (dpf) but ZZ fish directly formed testes, avoiding a juvenile ovary phase. Gonads of some ZW and WW fish, however, developed oocytes that died as the gonad became a testis, mimicking AB fish, suggesting that the gynogenetically derived AB strain is chromosomally WW. Single-cell RNA-seq of 19dpf gonads showed similar cell types in ZZ and ZW fish, including germ cells, precursors of gonadal support cells, steroidogenic cells, interstitial/stromal cells, and immune cells, consistent with a bipotential juvenile gonad. In contrast, scRNA-seq of 30dpf gonads revealed that cells in ZZ gonads had transcriptomes characteristic of testicular Sertoli, Leydig, and germ cells while ZW gonads had granulosa cells, theca cells, and developing oocytes. Hematopoietic and vascular cells were similar in both sex genotypes. These results show that juvenile NA zebrafish initially develop a bipotential gonad; that a factor on the NA W chromosome, or fewer than two Z chromosomes, is essential to initiate oocyte development; and without the W factor, or with two Z doses, NA gonads develop directly into testes without passing through the juvenile ovary stage. Sex determination in AB and TU strains mimics NA ZW and WW zebrafish, suggesting loss of the Z chromosome during domestication. Genetic analysis of the NA strain will facilitate our understanding of the evolution of sex determination mechanisms.
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23
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Dennhag N, Kahsay A, Nissen I, Nord H, Chermenina M, Liu J, Arner A, Liu JX, Backman LJ, Remeseiro S, von Hofsten J, Pedrosa Domellöf F. fhl2b mediates extraocular muscle protection in zebrafish models of muscular dystrophies and its ectopic expression ameliorates affected body muscles. Nat Commun 2024; 15:1950. [PMID: 38431640 PMCID: PMC10908798 DOI: 10.1038/s41467-024-46187-x] [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: 09/12/2023] [Accepted: 02/16/2024] [Indexed: 03/05/2024] Open
Abstract
In muscular dystrophies, muscle fibers loose integrity and die, causing significant suffering and premature death. Strikingly, the extraocular muscles (EOMs) are spared, functioning well despite the disease progression. Although EOMs have been shown to differ from body musculature, the mechanisms underlying this inherent resistance to muscle dystrophies remain unknown. Here, we demonstrate important differences in gene expression as a response to muscle dystrophies between the EOMs and trunk muscles in zebrafish via transcriptomic profiling. We show that the LIM-protein Fhl2 is increased in response to the knockout of desmin, plectin and obscurin, cytoskeletal proteins whose knockout causes different muscle dystrophies, and contributes to disease protection of the EOMs. Moreover, we show that ectopic expression of fhl2b can partially rescue the muscle phenotype in the zebrafish Duchenne muscular dystrophy model sapje, significantly improving their survival. Therefore, Fhl2 is a protective agent and a candidate target gene for therapy of muscular dystrophies.
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Affiliation(s)
- Nils Dennhag
- Department of Medical and Translational Biology, Umeå University, Umeå, Sweden
- Department of Clinical Sciences, Ophthalmology, Umeå University, Umeå, Sweden
| | - Abraha Kahsay
- Department of Medical and Translational Biology, Umeå University, Umeå, Sweden
- Department of Clinical Sciences, Ophthalmology, Umeå University, Umeå, Sweden
| | - Itzel Nissen
- Department of Medical and Translational Biology; Section of Molecular Medicine, Umeå University, Umeå, Sweden
- Wallenberg Center for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Hanna Nord
- Department of Medical and Translational Biology, Umeå University, Umeå, Sweden
| | - Maria Chermenina
- Department of Medical and Translational Biology, Umeå University, Umeå, Sweden
- Department of Clinical Sciences, Ophthalmology, Umeå University, Umeå, Sweden
| | - Jiao Liu
- Div. Thoracic Surgery, Dept. Clinical Sciences, Lund University, Lund, Sweden
- College of Life Sciences, South-Central University for Nationalities, Wuhan, China
| | - Anders Arner
- Div. Thoracic Surgery, Dept. Clinical Sciences, Lund University, Lund, Sweden
| | - Jing-Xia Liu
- Department of Medical and Translational Biology, Umeå University, Umeå, Sweden
| | - Ludvig J Backman
- Department of Medical and Translational Biology, Umeå University, Umeå, Sweden
| | - Silvia Remeseiro
- Department of Medical and Translational Biology; Section of Molecular Medicine, Umeå University, Umeå, Sweden
- Wallenberg Center for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Jonas von Hofsten
- Department of Medical and Translational Biology, Umeå University, Umeå, Sweden.
| | - Fatima Pedrosa Domellöf
- Department of Medical and Translational Biology, Umeå University, Umeå, Sweden.
- Department of Clinical Sciences, Ophthalmology, Umeå University, Umeå, Sweden.
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24
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Jimenez-Gonzalez A, Ansaloni F, Nebendahl C, Alavioon G, Murray D, Robak W, Sanges R, Müller F, Immler S. Paternal starvation affects metabolic gene expression during zebrafish offspring development and lifelong fitness. Mol Ecol 2024; 33:e17296. [PMID: 38361456 DOI: 10.1111/mec.17296] [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: 09/19/2023] [Revised: 01/03/2024] [Accepted: 01/12/2024] [Indexed: 02/17/2024]
Abstract
Dietary restriction in the form of fasting is a putative key to a healthier and longer life, but these benefits may come at a trade-off with reproductive fitness and may affect the following generation(s). The potential inter- and transgenerational effects of long-term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split-egg clutch design to explore the male-specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected, we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 h post-fertilisation in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra-embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism-associated genes. These similarities suggest a physiologically relevant, directed and potentially adaptive response transmitted by the father, independently from the offspring's nutritional state, which was defined by the mother.
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Affiliation(s)
- Ada Jimenez-Gonzalez
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Federico Ansaloni
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | | | - Ghazal Alavioon
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
| | - David Murray
- School of Biological Sciences, University of East Anglia, Norwich, UK
- Centre for Environment, Fisheries, and Aquaculture Science, Lowestoft, UK
| | - Weronika Robak
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Remo Sanges
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Simone Immler
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
- School of Biological Sciences, University of East Anglia, Norwich, UK
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25
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Gaidhani PM, Chakraborty S, Ramesh K, Velayudhaperumal Chellam P, van Hullebusch ED. Molecular interactions of paraben family of pollutants with embryonic neuronal proteins of Danio rerio: A step ahead in computational toxicity towards adverse outcome pathway. CHEMOSPHERE 2024; 351:141155. [PMID: 38211790 DOI: 10.1016/j.chemosphere.2024.141155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/28/2023] [Accepted: 01/07/2024] [Indexed: 01/13/2024]
Abstract
The paraben family of endocrine disruptors exhibit persistent behaviours in aquatic matrices, having bio-accumulative effects and necessitating toxicity analysis and safe use, as well as prevention of food web penetration. In this study, the toxicity effects of 9 different parabens (Methyl, Ethyl, Propyl, Butyl, Heptyl, Isopropyl, Isobutyl, benzyl parabens and p-hydroxybenzoic acid) were studied against 17 neuronal proteins (Neurog1, Ascl1a, DLA, Syn2a, Ntn1a, Pitx2, and SoxB1, Her/Hes, Zic family) expressed during the early embryonic developmental stage of Danio rerio. The neuronal genes were selected as a biomarker to study the inhibitory effects on the cascade of genes expressed in the early developmental stage. The study uses trRossetta software to predict protein structures of neuronal genes, followed by structural refinement, energy minimisation, and active site prediction, evaluated using energy value, RC plot and ERRAT scores of PROCHECK and ERRAT programs. Compared to raw structures, highly confident predicted structures and quality scores were observed for refined protein with few exceptions. Based on the polarity and charge of the aminoacids, the probable pockets were identified using active site prediction, which were then used for molecular docking analysis. Further, the ADMET analysis, ligand likeliness and toxicological test revealed the paraben family of compounds as one of the most susceptible toxic and mutagenic compounds. The molecular docking results showed an interesting pattern of increasing binding affinity with increase in the carbon chains of paraben molecules. Benzyl Paraben showed higher binding affinities across all 17 neuronal proteins. Finally, gene co-occurrence/co-expression and protein-protein interaction studies using the STRING database depict that all proteins are functionally related and play essential roles in standard biological processes or pathways, conserved and expressed in diverse organisms. The interaction between paraben compounds and neuronal genes indicates high risks of inhibiting reactions in embryonic stages, emphasising the need for effective treatment measures and strict regulations.
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Affiliation(s)
- Prerna Mahesh Gaidhani
- Water Research Group, Department of Bioengineering, National Institute of Technology Agartala, India
| | - Swastik Chakraborty
- Water Research Group, Department of Bioengineering, National Institute of Technology Agartala, India
| | - Kheerthana Ramesh
- Water Research Group, Department of Bioengineering, National Institute of Technology Agartala, India
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26
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Fuentes‐Pardo AP, Stanley R, Bourne C, Singh R, Emond K, Pinkham L, McDermid JL, Andersson L, Ruzzante DE. Adaptation to seasonal reproduction and environment-associated factors drive temporal and spatial differentiation in northwest Atlantic herring despite gene flow. Evol Appl 2024; 17:e13675. [PMID: 38495946 PMCID: PMC10940790 DOI: 10.1111/eva.13675] [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: 02/08/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Understanding how marine organisms adapt to local environments is crucial for predicting how populations will respond to global climate change. The genomic basis, environmental factors and evolutionary processes involved in local adaptation are however not well understood. Here we use Atlantic herring, an abundant, migratory and widely distributed marine fish with substantial genomic resources, as a model organism to evaluate local adaptation. We examined genomic variation and its correlation with environmental variables across a broad environmental gradient, for 15 spawning aggregations in Atlantic Canada and the United States. We then compared our results with available genomic data of northeast Atlantic populations. We confirmed that population structure lies in a fraction of the genome including likely adaptive genetic variants of functional importance. We discovered 10 highly differentiated genomic regions distributed across four chromosomes. Nine regions show strong association with seasonal reproduction. One region, corresponding to a known inversion on chromosome 12, underlies a latitudinal pattern discriminating populations north and south of a biogeographic transition zone on the Scotian Shelf. Genome-environment associations indicate that winter seawater temperature best correlates with the latitudinal pattern of this inversion. The variation at two so-called 'islands of divergence' related to seasonal reproduction appear to be private to the northwest Atlantic. Populations in the northwest and northeast Atlantic share variation at four of these divergent regions, simultaneously displaying significant diversity in haplotype composition at another four regions, which includes an undescribed structural variant approximately 7.7 Mb long on chromosome 8. Our results suggest that the timing and geographic location of spawning and early development may be under diverse selective pressures related to allelic fitness across environments. Our study highlights the role of genomic architecture, ancestral haplotypes and selection in maintaining adaptive divergence in species with large population sizes and presumably high gene flow.
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Affiliation(s)
- Angela P. Fuentes‐Pardo
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Ryan Stanley
- Fisheries and Oceans CanadaMaritimes RegionDartmouthNova ScotiaCanada
| | - Christina Bourne
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt John'sNewfoundland and LabradorCanada
| | - Rabindra Singh
- Fisheries and Oceans CanadaSt. Andrews Biological StationSt. AndrewsNew BrunswickCanada
| | - Kim Emond
- Fisheries and Oceans CanadaMaurice Lamontagne InstituteMont‐JoliQuebecCanada
| | - Lisa Pinkham
- Department of Marine ResourcesWest Boothbay HarborMaineUSA
| | - Jenni L. McDermid
- Fisheries and Oceans CanadaGulf Fisheries CentreMonctonNew BrunswickCanada
| | - Leif Andersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
- Department of Veterinary Integrative BiosciencesTexas A&M UniversityCollege StationTexasUSA
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27
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Uribe RA. Genetic regulation of enteric nervous system development in zebrafish. Biochem Soc Trans 2024; 52:177-190. [PMID: 38174765 PMCID: PMC10903509 DOI: 10.1042/bst20230343] [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: 08/29/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024]
Abstract
The enteric nervous system (ENS) is a complex series of interconnected neurons and glia that reside within and along the entire length of the gastrointestinal tract. ENS functions are vital to gut homeostasis and digestion, including local control of peristalsis, water balance, and intestinal cell barrier function. How the ENS develops during embryological development is a topic of great concern, as defects in ENS development can result in various diseases, the most common being Hirschsprung disease, in which variable regions of the infant gut lack ENS, with the distal colon most affected. Deciphering how the ENS forms from its progenitor cells, enteric neural crest cells, is an active area of research across various animal models. The vertebrate animal model, zebrafish, has been increasingly leveraged to understand early ENS formation, and over the past 20 years has contributed to our knowledge of the genetic regulation that underlies enteric development. In this review, I summarize our knowledge regarding the genetic regulation of zebrafish enteric neuronal development, and based on the most current literature, present a gene regulatory network inferred to underlie its construction. I also provide perspectives on areas for future zebrafish ENS research.
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Affiliation(s)
- Rosa A. Uribe
- Biosciences Department, Rice University, Houston, TX 77005, U.S.A
- Laboratory of Neural Crest and Enteric Nervous System Development, Rice University, Houston, TX 77005, U.S.A
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28
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Abrar M, Ali S, Hussain I, Khatoon H, Batool F, Ghazanfar S, Corcoran D, Kawakami Y, Abbasi AA. Cis-regulatory control of mammalian Trps1 gene expression. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024. [PMID: 38369890 DOI: 10.1002/jez.b.23246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 12/22/2023] [Accepted: 01/31/2024] [Indexed: 02/20/2024]
Abstract
TRPS1 serves as the causative gene for tricho-rhino phalangeal syndrome, known for its craniofacial and skeletal abnormalities. The Trps1 gene encodes a protein that represses Wnt signaling through strong interactions with Wnt signaling inhibitors. The identification of genomic cis-acting regulatory sequences governing Trps1 expression is crucial for understanding its role in embryogenesis. Nevertheless, to date, no investigations have been conducted concerning these aspects of Trps1. To identify deeply conserved noncoding elements (CNEs) within the Trps1 locus, we employed a comparative genomics approach, utilizing slowly evolving fish such as coelacanth and spotted gar. These analyses resulted in the identification of eight CNEs in the intronic region of the Trps1 gene. Functional characterization of these CNEs in zebrafish revealed their regulatory potential in various tissues, including pectoral fins, heart, and pharyngeal arches. RNA in-situ hybridization experiments revealed concordance between the reporter expression pattern induced by the identified set of CNEs and the spatial expression pattern of the trps1 gene in zebrafish. Comparative in vivo data from zebrafish and mice for CNE7/hs919 revealed conserved functions of these enhancers. Each of these eight CNEs was further investigated in cell line-based reporter assays, revealing their repressive potential. Taken together, in vivo and in vitro assays suggest a context-dependent dual functionality for the identified set of Trps1-associated CNE enhancers. This functionally characterized set of CNE-enhancers will contribute to a more comprehensive understanding of the developmental roles of Trps1 and can aid in the identification of noncoding DNA variants associated with human diseases.
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Affiliation(s)
- Muhammad Abrar
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shahid Ali
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, USA
| | - Irfan Hussain
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Center of Regenerative Medicine and Stem Cells Research, Aga Khan University Hospital, Karachi, Pakistan
| | - Hizran Khatoon
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fatima Batool
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shakira Ghazanfar
- National Institute for Genomics Advanced Biotechnology, National Agriculture Research Centre (NARC), Islamabad, Pakistan
| | - Dylan Corcoran
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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29
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Rogers CD, Amemiya C, Arur S, Babonis L, Barresi M, Bartlett M, Behringer R, Benham-Pyle B, Bergmann D, Blackman B, Brown CT, Browne B, Camacho J, Chabu CY, Chow I, Cleaver O, Cool J, Dennis MY, Dickinson AJ, Di Talia S, Frank M, Gillmor S, Haag ES, Hariharan I, Harland R, Husbands A, Jerome-Majewska L, Koenig K, Labonne C, Layden M, Lowe C, Mani M, Martik M, McKown K, Moens C, Mosimann C, Onyenedum J, Reed R, Rivera A, Rokhsar D, Royer L, Rutaganira F, Shahan R, Sinha N, Swalla B, Van Norman JM, Wagner DE, Wikramanayake A, Zebell S, Brady SM. Pluripotency of a founding field: rebranding developmental biology. Development 2024; 151:dev202342. [PMID: 38345109 PMCID: PMC10986740 DOI: 10.1242/dev.202342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
The field of developmental biology has declined in prominence in recent decades, with off-shoots from the field becoming more fashionable and highly funded. This has created inequity in discovery and opportunity, partly due to the perception that the field is antiquated or not cutting edge. A 'think tank' of scientists from multiple developmental biology-related disciplines came together to define specific challenges in the field that may have inhibited innovation, and to provide tangible solutions to some of the issues facing developmental biology. The community suggestions include a call to the community to help 'rebrand' the field, alongside proposals for additional funding apparatuses, frameworks for interdisciplinary innovative collaborations, pedagogical access, improved science communication, increased diversity and inclusion, and equity of resources to provide maximal impact to the community.
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Affiliation(s)
- Crystal D. Rogers
- Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
| | - Chris Amemiya
- University of California, Merced, Department of Molecular and Cell Biology and Quantitative and Systems Biology Program, 5200 N. Lake Road, SE1 262, Merced, CA 95343, USA
| | - Swathi Arur
- The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Leslie Babonis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | | | - Madelaine Bartlett
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Richard Behringer
- The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Blair Benham-Pyle
- Stem Cell and Regenerative Medicine Center, Baylor College of Medicine, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dominique Bergmann
- Department of Biology and HHMI, Stanford University, Stanford, CA 94305, USA
| | - Ben Blackman
- University of California, Berkeley, Berkeley CA 94720, USA
| | - C. Titus Brown
- Population Health & Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
| | - Bill Browne
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | - Jasmin Camacho
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Ida Chow
- Society for Developmental Biology, Rockville, MD 20852, USA
| | - Ondine Cleaver
- Department of Molecular Biology, Center for Regenerative Science and Medicine, UT Southwestern Medical School, Dallas, TX 75390, USA
| | - Jonah Cool
- Chan Zuckerberg Initiative, Redwood City, CA 94063, USA
| | - Megan Y. Dennis
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Alexandra Jazz Dickinson
- Department of Cell and Developmental Biology, School of Biological Science, University of California San Diego, La Jolla, CA 92093, USA
| | - Stefano Di Talia
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Margaret Frank
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Stewart Gillmor
- Unidad de Genómica Avanzada, CINVESTAV-IPN, Irapuato, Guanajuato 36824, Mexico
| | - Eric S. Haag
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Iswar Hariharan
- University of California Berkeley, Department of Molecular and Cell Biology, Berkeley, CA 94720, USA
| | - Richard Harland
- University of California Berkeley, Department of Molecular and Cell Biology, Berkeley, CA 94720, USA
| | - Aman Husbands
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Loydie Jerome-Majewska
- Department of Pediatrics, Human Genetics, Anatomy and Cell Biology, McGill University and Research Institute of the McGill University Health Centre at Glen Site, Montreal, QC H4A 3J1, Canada
| | | | - Carole Labonne
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Michael Layden
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Chris Lowe
- Hopkins Marine Station, Department of Biology, Stanford University, 120 Oceanview Blvd., Pacific Grove, CA 93950, USA
| | - Madhav Mani
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Megan Martik
- University of California Berkeley, Department of Molecular and Cell Biology, Berkeley, CA 94720, USA
| | - Katelyn McKown
- Department of Biology and Stanford Introductory Studies, Stanford University, Stanford, CA 94305, USA
| | - Cecilia Moens
- Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Christian Mosimann
- Children's Hospital Colorado, Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Anschutz Medical Campus, 12801 E. 17th Avenue, RC1 South, 12114, Aurora, CO 80045, USA
| | - Joyce Onyenedum
- School of Integrative Plant Sciences and L. H. Bailey Hortorium, Cornell University, Ithaca, NY 14853, USA
| | - Robert Reed
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Ajna Rivera
- University of the Pacific, Stockton, CA 95211, USA
| | - Dan Rokhsar
- University of California Berkeley, Department of Molecular and Cell Biology, Berkeley, CA 94720, USA
| | - Loic Royer
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Flora Rutaganira
- Departments of Biochemistry and Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Rachel Shahan
- Department of Biology, Duke University, Durham, NC 27708, USA
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Neelima Sinha
- Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Billie Swalla
- Biology Department and Friday Harbor Labs, University of Washington, Seattle, WA 98195, USA
| | - Jaimie M. Van Norman
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Daniel E. Wagner
- Department of Obstetrics, Gynecology and Reproductive Science, University of California, San Francisco, CA 94143, USA
| | | | - Sophia Zebell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Siobhán M. Brady
- Department of Plant Biology and Genome Center, University of California, Davis, CA 95616, USA
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30
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He J, Blazeski A, Nilanthi U, Menéndez J, Pirani SC, Levic DS, Bagnat M, Singh MK, Raya JG, García-Cardeña G, Torres-Vázquez J. Plxnd1-mediated mechanosensing of blood flow controls the caliber of the Dorsal Aorta via the transcription factor Klf2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.576555. [PMID: 38328196 PMCID: PMC10849625 DOI: 10.1101/2024.01.24.576555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The cardiovascular system generates and responds to mechanical forces. The heartbeat pumps blood through a network of vascular tubes, which adjust their caliber in response to the hemodynamic environment. However, how endothelial cells in the developing vascular system integrate inputs from circulatory forces into signaling pathways to define vessel caliber is poorly understood. Using vertebrate embryos and in vitro-assembled microvascular networks of human endothelial cells as models, flow and genetic manipulations, and custom software, we reveal that Plexin-D1, an endothelial Semaphorin receptor critical for angiogenic guidance, employs its mechanosensing activity to serve as a crucial positive regulator of the Dorsal Aorta's (DA) caliber. We also uncover that the flow-responsive transcription factor KLF2 acts as a paramount mechanosensitive effector of Plexin-D1 that enlarges endothelial cells to widen the vessel. These findings illuminate the molecular and cellular mechanisms orchestrating the interplay between cardiovascular development and hemodynamic forces.
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Affiliation(s)
- Jia He
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Adriana Blazeski
- Center for Excellence in Vascular Biology, Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA and Harvard Medical School, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Uthayanan Nilanthi
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857
| | - Javier Menéndez
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Samuel C. Pirani
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Daniel S. Levic
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
| | - Michel Bagnat
- Department of Cell Biology, Duke University, Durham, NC 27710, USA
| | - Manvendra K. Singh
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, 8 College Road, Singapore, 169857
- National Heart Research Institute Singapore, National Heart Centre Singapore, 5 Hospital Drive, Singapore, 169609
| | - José G Raya
- Department of Radiology, New York University School of Medicine, New York, NY 10016, USA
| | - Guillermo García-Cardeña
- Center for Excellence in Vascular Biology, Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA and Harvard Medical School, Boston, MA, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jesús Torres-Vázquez
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA
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31
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Peloggia J, Lush ME, Tsai YY, Wood C, Piotrowski T. Environmental and molecular control of tissue-specific ionocyte differentiation in zebrafish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.12.575421. [PMID: 38260427 PMCID: PMC10802608 DOI: 10.1101/2024.01.12.575421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Organisms adjust their physiology to cope with environmental fluctuations and maintain fitness. These adaptations occur via genetic changes over multiple generations or through acclimation, a set of reversible phenotypic changes that confer resilience to the individual. Aquatic organisms are subject to dramatic seasonal fluctuations in water salinity, which can affect the function of lateral line mechanosensory hair cells. To maintain hair cell function when salinity decreases, ion-regulating cells, Neuromast-associated ionocytes (Nm ionocytes), increase in number and invade lateral line neuromasts. How environmental changes trigger this adaptive differentiation of Nm ionocytes and how these cells are specified is still unknown. Here, we identify Nm ionocyte progenitors as foxi3a/foxi3b-expressing skin cells and show that their differentiation is associated with sequential activation of different Notch pathway components, which control ionocyte survival. We demonstrate that new Nm ionocytes are rapidly specified by absolute salinity levels, independently of stress response pathways. We further show that Nm ionocyte differentiation is selectively triggered by depletion of specific ions, such as Ca2+ and Na+/Cl-, but not by low K+ levels, and is independent of media osmolarity. Finally, we demonstrate that hair cell activity plays a role in Nm ionocyte recruitment and that systemic factors are not necessary for Nm ionocyte induction. In summary, we have identified how environmental changes activate a signaling cascade that triggers basal skin cell progenitors to differentiate into Nm ionocytes and invade lateral line organs. This adaptive behavior is an example of physiological plasticity that may prove essential for survival in changing climates.
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Affiliation(s)
- Julia Peloggia
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Mark E. Lush
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ya-Yin Tsai
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Christopher Wood
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Tatjana Piotrowski
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Lead Contact
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32
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Putman TE, Schaper K, Matentzoglu N, Rubinetti V, Alquaddoomi F, Cox C, Caufield JH, Elsarboukh G, Gehrke S, Hegde H, Reese J, Braun I, Bruskiewich R, Cappelletti L, Carbon S, Caron A, Chan L, Chute C, Cortes K, De Souza V, Fontana T, Harris N, Hartley E, Hurwitz E, Jacobsen JB, Krishnamurthy M, Laraway B, McLaughlin J, McMurry J, Moxon ST, Mullen K, O’Neil S, Shefchek K, Stefancsik R, Toro S, Vasilevsky N, Walls R, Whetzel P, Osumi-Sutherland D, Smedley D, Robinson P, Mungall C, Haendel M, Munoz-Torres M. The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species. Nucleic Acids Res 2024; 52:D938-D949. [PMID: 38000386 PMCID: PMC10767791 DOI: 10.1093/nar/gkad1082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/21/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and understanding mechanisms of diseases. It requires integrating open data at a global scale. The Monarch Initiative advances these goals by developing open ontologies, semantic data models, and knowledge graphs for translational research. The Monarch App is an integrated platform combining data about genes, phenotypes, and diseases across species. Monarch's APIs enable access to carefully curated datasets and advanced analysis tools that support the understanding and diagnosis of disease for diverse applications such as variant prioritization, deep phenotyping, and patient profile-matching. We have migrated our system into a scalable, cloud-based infrastructure; simplified Monarch's data ingestion and knowledge graph integration systems; enhanced data mapping and integration standards; and developed a new user interface with novel search and graph navigation features. Furthermore, we advanced Monarch's analytic tools by developing a customized plugin for OpenAI's ChatGPT to increase the reliability of its responses about phenotypic data, allowing us to interrogate the knowledge in the Monarch graph using state-of-the-art Large Language Models. The resources of the Monarch Initiative can be found at monarchinitiative.org and its corresponding code repository at github.com/monarch-initiative/monarch-app.
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Affiliation(s)
- Tim E Putman
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kevin Schaper
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Vincent P Rubinetti
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Faisal S Alquaddoomi
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Corey Cox
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - J Harry Caufield
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Glass Elsarboukh
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sarah Gehrke
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Harshad Hegde
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Justin T Reese
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ian Braun
- Data Collaboration Center, Critical Path Institute, Tucson, AZ 85718, USA
| | | | | | - Seth Carbon
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anita R Caron
- European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Lauren E Chan
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Christopher G Chute
- Schools of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Katherina G Cortes
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Tommaso Fontana
- Dipartimento di Informatica, Università degli Studi di Milano Statale, Milano, Italy
| | - Nomi L Harris
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emily L Hartley
- Data Collaboration Center, Critical Path Institute, Tucson, AZ 85718, USA
| | - Eric Hurwitz
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Julius O B Jacobsen
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Madan Krishnamurthy
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Bryan J Laraway
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Julie A McMurry
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sierra A T Moxon
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kathleen R Mullen
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Shawn T O’Neil
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kent A Shefchek
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ray Stefancsik
- European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Sabrina Toro
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Ramona L Walls
- Data Collaboration Center, Critical Path Institute, Tucson, AZ 85718, USA
| | - Patricia L Whetzel
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Damian Smedley
- William Harvey Research Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 6032, USA
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Melissa A Haendel
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Monica C Munoz-Torres
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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33
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Badaczewska-Dawid AE, Kuriata A, Pintado-Grima C, Garcia-Pardo J, Burdukiewicz M, Iglesias V, Kmiecik S, Ventura S. A3D Model Organism Database (A3D-MODB): a database for proteome aggregation predictions in model organisms. Nucleic Acids Res 2024; 52:D360-D367. [PMID: 37897355 PMCID: PMC10767922 DOI: 10.1093/nar/gkad942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/27/2023] [Accepted: 10/11/2023] [Indexed: 10/30/2023] Open
Abstract
Protein aggregation has been associated with aging and different pathologies and represents a bottleneck in the industrial production of biotherapeutics. Numerous past studies performed in Escherichia coli and other model organisms have allowed to dissect the biophysical principles underlying this process. This knowledge fuelled the development of computational tools, such as Aggrescan 3D (A3D) to forecast and re-design protein aggregation. Here, we present the A3D Model Organism Database (A3D-MODB) http://biocomp.chem.uw.edu.pl/A3D2/MODB, a comprehensive resource for the study of structural protein aggregation in the proteomes of 12 key model species spanning distant biological clades. In addition to A3D predictions, this resource incorporates information useful for contextualizing protein aggregation, including membrane protein topology and structural model confidence, as an indirect reporter of protein disorder. The database is openly accessible without any need for registration. We foresee A3D-MOBD evolving into a central hub for conducting comprehensive, multi-species analyses of protein aggregation, fostering the development of protein-based solutions for medical, biotechnological, agricultural and industrial applications.
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Affiliation(s)
| | - Aleksander Kuriata
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Carlos Pintado-Grima
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Javier Garcia-Pardo
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Michał Burdukiewicz
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
- Clinical Research Centre, Medical University of Białystok, Kilińskiego 1, 15-369, Białystok, Poland
| | - Valentín Iglesias
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Sebastian Kmiecik
- Biological and Chemical Research Center, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina (IBB) and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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34
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Heidarian Y, Tourigny JP, Fasteen TD, Mahmoudzadeh NH, Hurlburt AJ, Nemkov T, Reisz JA, D’Alessandro A, Tennessen JM. Metabolomic analysis of Drosophila melanogaster larvae lacking pyruvate kinase. G3 (BETHESDA, MD.) 2023; 14:jkad228. [PMID: 37792629 PMCID: PMC10755183 DOI: 10.1093/g3journal/jkad228] [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: 06/02/2023] [Revised: 06/02/2023] [Accepted: 09/24/2023] [Indexed: 10/06/2023]
Abstract
Pyruvate kinase (Pyk) is a rate-limiting enzyme that catalyzes the final metabolic reaction in glycolysis. The importance of this enzyme, however, extends far beyond ATP production, as Pyk is also known to regulate tissue growth, cell proliferation, and development. Studies of this enzyme in Drosophila melanogaster are complicated by the fact that the fly genome encodes 6 Pyk paralogs whose functions remain poorly defined. To address this issue, we used sequence distance and phylogenetic approaches to demonstrate that the gene Pyk encodes the enzyme most similar to the mammalian Pyk orthologs, while the other 5 Drosophila Pyk paralogs have significantly diverged from the canonical enzyme. Consistent with this observation, metabolomic studies of 2 different Pyk mutant strains revealed that larvae lacking Pyk exhibit a severe block in glycolysis, with a buildup of glycolytic intermediates upstream of pyruvate. However, our analysis also unexpectedly reveals that pyruvate levels are unchanged in Pyk mutants, indicating that larval metabolism maintains pyruvate pool size despite severe metabolic limitations. Consistent with our metabolomic findings, a complementary RNA-seq analysis revealed that genes involved in lipid metabolism and protease activity are elevated in Pyk mutants, again indicating that loss of this glycolytic enzyme induces compensatory changes in other aspects of metabolism. Overall, our study provides both insight into how Drosophila larval metabolism adapts to disruption of glycolytic metabolism as well as immediate clinical relevance, considering that Pyk deficiency is the most common congenital enzymatic defect in humans.
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Affiliation(s)
- Yasaman Heidarian
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Jason P Tourigny
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Tess D Fasteen
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | | | | | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Julie A Reisz
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Angelo D’Alessandro
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jason M Tennessen
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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35
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Leary JR, Bacher R. Interpretable trajectory inference with single-cell Linear Adaptive Negative-binomial Expression (scLANE) testing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572477. [PMID: 38187622 PMCID: PMC10769309 DOI: 10.1101/2023.12.19.572477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The rapid proliferation of trajectory inference methods for single-cell RNA-seq data has allowed researchers to investigate complex biological processes by examining underlying gene expression dynamics. After estimating a latent cell ordering, statistical models are used to determine which genes exhibit changes in expression that are significantly associated with progression through the biological trajectory. While a few techniques for performing trajectory differential expression exist, most rely on the flexibility of generalized additive models in order to account for the inherent nonlinearity of changes in gene expression. As such, the results can be difficult to interpret, and biological conclusions often rest on subjective visual inspections of the most dynamic genes. To address this challenge, we propose scLANE testing, which is built around an interpretable generalized linear model and handles nonlinearity with basis splines chosen empirically for each gene. In addition, extensions to estimating equations and mixed models allow for reliable trajectory testing under complex experimental designs. After validating the accuracy of scLANE under several different simulation scenarios, we apply it to a set of diverse biological datasets and display its ability to provide novel biological information when used downstream of both pseudotime and RNA velocity estimation methods.
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Affiliation(s)
- Jack R. Leary
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, USA
| | - Rhonda Bacher
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, USA
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36
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Madera D, Alonso-Gómez A, Delgado MJ, Valenciano AI, Alonso-Gómez ÁL. Gene Characterization of Nocturnin Paralogues in Goldfish: Full Coding Sequences, Structure, Phylogeny and Tissue Expression. Int J Mol Sci 2023; 25:54. [PMID: 38203224 PMCID: PMC10779419 DOI: 10.3390/ijms25010054] [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: 10/30/2023] [Revised: 12/05/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
The aim of this work is the full characterization of all the nocturnin (noc) paralogues expressed in a teleost, the goldfish. An in silico analysis of the evolutive origin of noc in Osteichthyes is performed, including the splicing variants and new paralogues appearing after teleostean 3R genomic duplication and the cyprinine 4Rc. After sequencing the full-length mRNA of goldfish, we obtained two isoforms for noc-a (noc-aa and noc-ab) with two splice variants (I and II), and only one for noc-b (noc-bb) with two transcripts (II and III). Using the splicing variant II, the prediction of the secondary and tertiary structures renders a well-conserved 3D distribution of four α-helices and nine β-sheets in the three noc isoforms. A synteny analysis based on the localization of noc genes in the patrilineal or matrilineal subgenomes and a phylogenetic tree of protein sequences were accomplished to stablish a classification and a long-lasting nomenclature of noc in goldfish, and valid to be extrapolated to allotetraploid Cyprininae. Finally, both goldfish and zebrafish showed a broad tissue expression of all the noc paralogues. Moreover, the enriched expression of specific paralogues in some tissues argues in favour of neo- or subfunctionalization.
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Affiliation(s)
| | | | | | | | - Ángel Luis Alonso-Gómez
- Departamento de Genética, Fisiología y Microbiología, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.M.); (A.A.-G.); (M.J.D.); (A.I.V.)
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37
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Sur A, Wang Y, Capar P, Margolin G, Prochaska MK, Farrell JA. Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development. Dev Cell 2023; 58:3028-3047.e12. [PMID: 37995681 PMCID: PMC11181902 DOI: 10.1016/j.devcel.2023.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/24/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023]
Abstract
During development, animals generate distinct cell populations with specific identities, functions, and morphologies. We mapped transcriptionally distinct populations across 489,686 cells from 62 stages during wild-type zebrafish embryogenesis and early larval development (3-120 h post-fertilization). Using these data, we identified the limited catalog of gene expression programs reused across multiple tissues and their cell-type-specific adaptations. We also determined the duration each transcriptional state is present during development and identify unexpected long-term cycling populations. Focused clustering and transcriptional trajectory analyses of non-skeletal muscle and endoderm identified transcriptional profiles and candidate transcriptional regulators of understudied cell types and subpopulations, including the pneumatic duct, individual intestinal smooth muscle layers, spatially distinct pericyte subpopulations, and recently discovered best4+ cells. To enable additional discoveries, we make this comprehensive transcriptional atlas of early zebrafish development available through our website, Daniocell.
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Affiliation(s)
- Abhinav Sur
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814, USA
| | - Yiqun Wang
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Paulina Capar
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814, USA
| | - Gennady Margolin
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814, USA
| | - Morgan Kathleen Prochaska
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814, USA
| | - Jeffrey A Farrell
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814, USA.
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38
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Khalili A, Safarian N, van Wijngaarden E, Zoidl GS, Zoidl GR, Rezai P. Loss of Panx1 function in zebrafish alters motor behavior in a lab-on-chip model of Parkinson's disease. J Neurosci Res 2023; 101:1814-1825. [PMID: 37688406 DOI: 10.1002/jnr.25241] [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: 12/20/2022] [Revised: 08/08/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023]
Abstract
Pannexin 1 (Panx1) forms ATP-permeable membrane channels that play roles in purinergic signaling in the nervous system. A link between Panx1 activity and neurodegenerative disorders including Parkinson's disease (PD) has been suggested, but experimental evidence is limited. Here, a zebrafish model of PD was produced by exposing panx1a+/+ and panx1a-/- zebrafish larvae to 6-hydroxydopamine (6-OHDA). Electrical stimulation in a microfluidic chip and quantitative real-time-qPCR of zebrafish larvae tested the role of Panx1 in both pathological and normal conditions. After 72-h treatment with 6-OHDA, the electric-induced locomotor activity of 5 days post fertilization (5dpf) panx1a+/+ larvae were reduced, while the stimulus did not affect locomotor activity of age-matched panx1a-/- larvae. A RT-qPCR analysis showed an increase in the expression of genes that are functionally related to dopaminergic signaling, like the tyrosine hydroxylase (th2) and the leucine-rich repeat kinase 2 (lrrk2). Extending the 6-OHDA treatment duration to 120 h caused a significant reduction in the locomotor response of 7dpf panx1a-/- larvae compared to the untreated panx1a-/- group. The RT-qPCR data showed a reduced expression of dopaminergic signaling genes in both genotypes. It was concluded that the absence of Panx1a channels compromised dopaminergic signaling in 6-OHDA-treated zebrafish larvae and that the increase in the expression of dopaminergic genes was transient, most likely due to a compensatory upregulation. We propose that zebrafish Panx1a models offer opportunities to shed light on PD's physiological and molecular basis. Panx1a might play a role on the progression of PD, and therefore deserves further investigation.
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Affiliation(s)
- Arezoo Khalili
- Department of Mechanical Engineering, York University, Toronto, Ontario, Canada
| | - Nickie Safarian
- Department of Biology, York University, Toronto, Ontario, Canada
| | | | - Georg S Zoidl
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Georg R Zoidl
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Pouya Rezai
- Department of Mechanical Engineering, York University, Toronto, Ontario, Canada
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da Cunha JI, Barauna AMD, Garcez RC. Prechordal structures act cooperatively in early trabeculae development of gnathostome skull. Cells Dev 2023; 176:203879. [PMID: 37844659 DOI: 10.1016/j.cdev.2023.203879] [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: 03/29/2023] [Revised: 10/04/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]
Abstract
The vertebrate skull is formed by mesoderm and neural crest (NC) cells. The mesoderm contributes to the skull chordal domain, with the notochord playing an essential role in this process. The NC contributes to the skull prechordal domain, prompting investigation into the embryonic structures involved in prechordal neurocranium cartilage formation. The trabeculae cartilage, a structure of the prechordal neurocranium, arises at the convergence of prechordal plate (PCP), ventral midline (VM) cells of the diencephalon, and dorsal oral ectoderm. This study examines the molecular participation of these embryonic structures in gnathostome trabeculae development. PCP-secreted SHH induces its expression in VM cells of the diencephalon, initiating a positive feedback loop involving SIX3 and GLI1. SHH secreted by the VM cells of the diencephalon acts on the dorsal oral ectoderm, stimulating condensation of NC cells to form trabeculae. SHH from the prechordal region affects the expression of SOX9 in NC cells. BMP7 and SHH secreted by PCP induce NKX2.1 expression in VM cells of the diencephalon, but this does not impact trabeculae formation. Molecular cooperation between PCP, VM cells of the diencephalon, and dorsal oral ectoderm is crucial for craniofacial development by NC cells in the prechordal domain.
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Affiliation(s)
- Jaqueline Isoppo da Cunha
- Graduate Program of Cell and Developmental Biology, Federal University of Santa Catarina, Florianopolis, SC, Brazil; Stem Cell and Tissue Regeneration Laboratory (LACERT), Federal University of Santa Catarina, Florianopolis, SC, Brazil
| | - Alessandra Maria Duarte Barauna
- Graduate Program of Cell and Developmental Biology, Federal University of Santa Catarina, Florianopolis, SC, Brazil; Stem Cell and Tissue Regeneration Laboratory (LACERT), Federal University of Santa Catarina, Florianopolis, SC, Brazil
| | - Ricardo Castilho Garcez
- Graduate Program of Cell and Developmental Biology, Federal University of Santa Catarina, Florianopolis, SC, Brazil; Stem Cell and Tissue Regeneration Laboratory (LACERT), Federal University of Santa Catarina, Florianopolis, SC, Brazil; Department of Cell Biology, Embryology, and Genetics, Federal University of Santa Catarina, Florianopolis, SC, Brazil.
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Kaya S, Alliston T, Evans DS. Genetic and Gene Expression Resources for Osteoporosis and Bone Biology Research. Curr Osteoporos Rep 2023; 21:637-649. [PMID: 37831357 PMCID: PMC11098148 DOI: 10.1007/s11914-023-00821-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/11/2023] [Indexed: 10/14/2023]
Abstract
PURPOSE OF REVIEW The integration of data from multiple genomic assays from humans and non-human model organisms is an effective approach to identify genes involved in skeletal fragility and fracture risk due to osteoporosis and other conditions. This review summarizes genome-wide genetic variation and gene expression data resources relevant to the discovery of genes contributing to skeletal fragility and fracture risk. RECENT FINDINGS Genome-wide association studies (GWAS) of osteoporosis-related traits are summarized, in addition to gene expression in bone tissues in humans and non-human organisms, with a focus on rodent models related to skeletal fragility and fracture risk. Gene discovery approaches using these genomic data resources are described. We also describe the Musculoskeletal Knowledge Portal (MSKKP) that integrates much of the available genomic data relevant to fracture risk. The available genomic resources provide a wealth of knowledge and can be analyzed to identify genes related to fracture risk. Genomic resources that would fill particular scientific gaps are discussed.
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Affiliation(s)
- Serra Kaya
- Department of Orthopedic Surgery, University of California, San Francisco, CA, USA
| | - Tamara Alliston
- Department of Orthopedic Surgery, University of California, San Francisco, CA, USA
| | - Daniel S Evans
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA.
- California Pacific Medical Center Research Institute, San Francisco, CA, USA.
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Kelly JJ, Wen H, Brehm P. Single-cell RNAseq analysis of spinal locomotor circuitry in larval zebrafish. eLife 2023; 12:RP89338. [PMID: 37975797 PMCID: PMC10656102 DOI: 10.7554/elife.89338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023] Open
Abstract
Identification of the neuronal types that form the specialized circuits controlling distinct behaviors has benefited greatly from the simplicity offered by zebrafish. Electrophysiological studies have shown that in addition to connectivity, understanding of circuitry requires identification of functional specializations among individual circuit components, such as those that regulate levels of transmitter release and neuronal excitability. In this study, we use single-cell RNA sequencing (scRNAseq) to identify the molecular bases for functional distinctions between motoneuron types that are causal to their differential roles in swimming. The primary motoneuron, in particular, expresses high levels of a unique combination of voltage-dependent ion channel types and synaptic proteins termed functional 'cassettes.' The ion channel types are specialized for promoting high-frequency firing of action potentials and augmented transmitter release at the neuromuscular junction, both contributing to greater power generation. Our transcriptional profiling of spinal neurons further assigns expression of this cassette to specific interneuron types also involved in the central circuitry controlling high-speed swimming and escape behaviors. Our analysis highlights the utility of scRNAseq in functional characterization of neuronal circuitry, in addition to providing a gene expression resource for studying cell type diversity.
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Affiliation(s)
- Jimmy J Kelly
- Vollum Institute, Oregon Health & Science UniversityPortlandUnited States
| | - Hua Wen
- Vollum Institute, Oregon Health & Science UniversityPortlandUnited States
| | - Paul Brehm
- Vollum Institute, Oregon Health & Science UniversityPortlandUnited States
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42
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Kim YI, O'Rourke R, Sagerström CG. scMultiome analysis identifies embryonic hindbrain progenitors with mixed rhombomere identities. eLife 2023; 12:e87772. [PMID: 37947350 PMCID: PMC10662952 DOI: 10.7554/elife.87772] [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: 03/16/2023] [Accepted: 11/09/2023] [Indexed: 11/12/2023] Open
Abstract
Rhombomeres serve to position neural progenitors in the embryonic hindbrain, thereby ensuring appropriate neural circuit formation, but the molecular identities of individual rhombomeres and the mechanism whereby they form has not been fully established. Here, we apply scMultiome analysis in zebrafish to molecularly resolve all rhombomeres for the first time. We find that rhombomeres become molecularly distinct between 10hpf (end of gastrulation) and 13hpf (early segmentation). While the embryonic hindbrain transiently contains alternating odd- versus even-type rhombomeres, our scMultiome analyses do not detect extensive odd versus even molecular characteristics in the early hindbrain. Instead, we find that each rhombomere displays a unique gene expression and chromatin profile. Prior to the appearance of distinct rhombomeres, we detect three hindbrain progenitor clusters (PHPDs) that correlate with the earliest visually observed segments in the hindbrain primordium that represent prospective rhombomere r2/r3 (possibly including r1), r4, and r5/r6, respectively. We further find that the PHPDs form in response to Fgf and RA morphogens and that individual PHPD cells co-express markers of multiple mature rhombomeres. We propose that the PHPDs contain mixed-identity progenitors and that their subdivision into individual rhombomeres requires the resolution of mixed transcription and chromatin states.
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Affiliation(s)
- Yong-Il Kim
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical SchoolAuroraUnited States
| | - Rebecca O'Rourke
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical SchoolAuroraUnited States
| | - Charles G Sagerström
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical SchoolAuroraUnited States
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43
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Desvignes T, Bista I, Herrera K, Landes A, Postlethwait JH. Cold-Driven Hemoglobin Evolution in Antarctic Notothenioid Fishes Prior to Hemoglobin Gene Loss in White-Blooded Icefishes. Mol Biol Evol 2023; 40:msad236. [PMID: 37879119 PMCID: PMC10651078 DOI: 10.1093/molbev/msad236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/08/2023] [Accepted: 10/18/2023] [Indexed: 10/27/2023] Open
Abstract
Expression of multiple hemoglobin isoforms with differing physiochemical properties likely helps species adapt to different environmental and physiological conditions. Antarctic notothenioid fishes inhabit the icy Southern Ocean and display fewer hemoglobin isoforms, each with less affinity for oxygen than temperate relatives. Reduced hemoglobin multiplicity was proposed to result from relaxed selective pressure in the cold, thermally stable, and highly oxygenated Antarctic waters. These conditions also permitted the survival and diversification of white-blooded icefishes, the only vertebrates living without hemoglobin. To understand hemoglobin evolution during adaptation to freezing water, we analyzed hemoglobin genes from 36 notothenioid genome assemblies. Results showed that adaptation to frigid conditions shaped hemoglobin gene evolution by episodic diversifying selection concomitant with cold adaptation and by pervasive evolution in Antarctic notothenioids compared to temperate relatives, likely a continuing adaptation to Antarctic conditions. Analysis of hemoglobin gene expression in adult hematopoietic organs in various temperate and Antarctic species further revealed a switch in hemoglobin gene expression underlying hemoglobin multiplicity reduction in Antarctic fish, leading to a single hemoglobin isoform in adult plunderfishes and dragonfishes, the sister groups to icefishes. The predicted high hemoglobin multiplicity in Antarctic fish embryos based on transcriptomic data, however, raises questions about the molecular bases and physiological implications of diverse hemoglobin isoforms in embryos compared to adults. This analysis supports the hypothesis that the last common icefish ancestor was vulnerable to detrimental mutations affecting the single ancestral expressed alpha- and beta-globin gene pair, potentially predisposing their subsequent loss.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Iliana Bista
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt 60325, Germany
- Senckenberg Research Institute, Frankfurt 60325, Germany
| | - Karina Herrera
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Audrey Landes
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
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Saunders LM, Srivatsan SR, Duran M, Dorrity MW, Ewing B, Linbo TH, Shendure J, Raible DW, Moens CB, Kimelman D, Trapnell C. Embryo-scale reverse genetics at single-cell resolution. Nature 2023; 623:782-791. [PMID: 37968389 PMCID: PMC10665197 DOI: 10.1038/s41586-023-06720-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 10/06/2023] [Indexed: 11/17/2023]
Abstract
The maturation of single-cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos1-4. A majority of these data, however, has been collected from wild-type embryos without an appreciation for the latent variation that is present in development. Here we present the 'zebrafish single-cell atlas of perturbed embryos': single-cell transcriptomic data from 1,812 individually resolved developing zebrafish embryos, encompassing 19 timepoints, 23 genetic perturbations and a total of 3.2 million cells. The high degree of replication in our study (eight or more embryos per condition) enables us to estimate the variance in cell type abundance organism-wide and to detect perturbation-dependent deviance in cell type composition relative to wild-type embryos. Our approach is sensitive to rare cell types, resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons, a cell population that comprises less than 1% of the embryo. Additionally, time-series profiling of individual mutants identified a group of brachyury-independent cells with strikingly similar transcriptomes to notochord sheath cells, leading to new hypotheses about early origins of the skull. We anticipate that standardized collection of high-resolution, organism-scale single-cell data from large numbers of individual embryos will enable mapping of the genetic dependencies of zebrafish cell types, while also addressing longstanding challenges in developmental genetics, including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals.
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Affiliation(s)
- Lauren M Saunders
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sanjay R Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Madeleine Duran
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michael W Dorrity
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Brent Ewing
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Tor H Linbo
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - David W Raible
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | | | - David Kimelman
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
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45
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Kearney SK, Berger A, Baker E. Aon: a service to augment Alliance Genome Resource data with additional species. BMC Res Notes 2023; 16:297. [PMID: 37891644 PMCID: PMC10604687 DOI: 10.1186/s13104-023-06577-8] [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: 02/14/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
OBJECTIVE Cross-species comparative genomics requires access to accurate homology data across the entire range of annotated genes. The Alliance of Genome Resources (AGR) provides an open-source and comprehensive database of homology data calculated using a wide array of algorithms at differing stringencies to elucidate orthologous relationships. However, the current AGR application program interface (API) is limited to five homology endpoints for nine species. While AGR provides a robust resource for several canonical species, its utility can be greatly enhanced by increased filtering and data processing options and incorporating additional species. RESULTS Here, we describe a novel API tool, AON, that expands access to the AGR orthology resource by creating a data structure that supports 50 additional endpoints. More importantly, it provides users with a framework for adding bespoke endpoints, custom species, and additional orthology data. We demonstrate AON's functionality by incorporating the service into the GeneWeaver ecosystem for supporting cross-species data analysis.
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Affiliation(s)
- Sophie K Kearney
- Department of Computer Science, Baylor University, One Bear Place Box 97356, Waco, 76798, USA
| | | | - Erich Baker
- Department of Computer Science, Baylor University, One Bear Place Box 97356, Waco, 76798, USA.
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46
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Pihlström S, Richardt S, Määttä K, Pekkinen M, Olkkonen VM, Mäkitie O, Mäkitie RE. SGMS2 in primary osteoporosis with facial nerve palsy. Front Endocrinol (Lausanne) 2023; 14:1224318. [PMID: 37886644 PMCID: PMC10598846 DOI: 10.3389/fendo.2023.1224318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/18/2023] [Indexed: 10/28/2023] Open
Abstract
Pathogenic heterozygous variants in SGMS2 cause a rare monogenic form of osteoporosis known as calvarial doughnut lesions with bone fragility (CDL). The clinical presentations of SGMS2-related bone pathology range from childhood-onset osteoporosis with low bone mineral density and sclerotic doughnut-shaped lesions in the skull to a severe spondylometaphyseal dysplasia with neonatal fractures, long-bone deformities, and short stature. In addition, neurological manifestations occur in some patients. SGMS2 encodes sphingomyelin synthase 2 (SMS2), an enzyme involved in the production of sphingomyelin (SM). This review describes the biochemical structure of SM, SM metabolism, and their molecular actions in skeletal and neural tissue. We postulate how disrupted SM gradient can influence bone formation and how animal models may facilitate a better understanding of SGMS2-related osteoporosis.
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Affiliation(s)
- Sandra Pihlström
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sampo Richardt
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kirsi Määttä
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Minna Pekkinen
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Children´s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Vesa M. Olkkonen
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Outi Mäkitie
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Children´s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Riikka E. Mäkitie
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Otorhinolaryngology – Head and Neck Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
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47
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Cusick JK, Alcaide J, Shi Y. The RELT Family of Proteins: An Increasing Awareness of Their Importance for Cancer, the Immune System, and Development. Biomedicines 2023; 11:2695. [PMID: 37893069 PMCID: PMC10603948 DOI: 10.3390/biomedicines11102695] [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: 08/15/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
This review highlights Receptor Expressed in Lymphoid Tissues (RELT), a Tumor Necrosis Factor Superfamily member, and its two paralogs, RELL1 and RELL2. Collectively, these three proteins are referred to as RELTfms and have gained much interest in recent years due to their association with cancer and other human diseases. A thorough knowledge of their physiological functions, including the ligand for RELT, is lacking, yet emerging evidence implicates RELTfms in a variety of processes including cytokine signaling and pathways that either promote cell death or survival. T cells from mice lacking RELT exhibit increased responses against tumors and increased inflammatory cytokine production, and multiple lines of evidence indicate that RELT may promote an immunosuppressive environment for tumors. The relationship of individual RELTfms in different cancers is not universal however, as evidence indicates that individual RELTfms may be risk factors in certain cancers yet appear to be protective in other cancers. RELTfms are important for a variety of additional processes related to human health including microbial pathogenesis, inflammation, behavior, reproduction, and development. All three proteins have been strongly conserved in all vertebrates, and this review aims to provide a clearer understanding of the current knowledge regarding these interesting proteins.
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Affiliation(s)
- John K. Cusick
- College of Medicine, California Northstate University, Elk Grove, CA 95757, USA
| | - Jessa Alcaide
- College of Medicine, California Northstate University, Elk Grove, CA 95757, USA
| | - Yihui Shi
- College of Medicine, California Northstate University, Elk Grove, CA 95757, USA
- California Pacific Medical Center Research Institute, Sutter Bay Hospitals, San Francisco, CA 94107, USA
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48
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Grigg AG, Lowi-Merri TM, Hutchings JA, Massey MD. Thermal variability induces sex-specific morphometric changes in zebrafish (Danio rerio). JOURNAL OF FISH BIOLOGY 2023; 103:839-850. [PMID: 37679944 DOI: 10.1111/jfb.15551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 08/02/2023] [Accepted: 08/30/2023] [Indexed: 09/09/2023]
Abstract
In nature, organisms are exposed to variable environmental conditions that impact their performance and fitness. Despite the ubiquity of environmental variability, substantial knowledge gaps in our understanding of organismal responses to nonconstant thermal regimes remain. In the present study, using zebrafish (Danio rerio) as a model organism, we applied geometric morphometric methods to examine how challenging but ecologically realistic diel thermal fluctuations experienced during different life stages influence adult body shape, size, and condition. Zebrafish were exposed to either thermal fluctuations (22-32°C) or a static optimal temperature (27°C) sharing the same thermal mean during an early period spanning embryonic and larval ontogeny (days 0-30), a later period spanning juvenile and adult ontogeny (days 31-210), or a combination of both. We found that body shape, size, and condition were affected by thermal variability, but these plasticity-mediated changes were dependent on the timing of ontogenetic exposure. Notably, after experiencing fluctuating temperatures during early ontogeny, females displayed a deeper abdomen while males displayed an elongated caudal peduncle region. Moreover, males displayed beneficial acclimation of body condition under lifelong fluctuating temperature exposure, whereas females did not. The present study, using ecologically realistic thermal regimes, provides insight into the timing of environmental experiences that generate phenotypic variation in zebrafish.
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Affiliation(s)
- A G Grigg
- Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - J A Hutchings
- Dalhousie University, Halifax, Nova Scotia, Canada
- Flødevigen Marine Research Station, Institute of Marine Research, Bergen, Norway
- Department of Natural Sciences, University of Agder, Kristiansand, Norway
| | - M D Massey
- Dalhousie University, Halifax, Nova Scotia, Canada
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49
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Anticevic I, Otten C, Vinkovic L, Jukic L, Popovic M. Tyrosyl-DNA phosphodiesterase 1 (TDP1) and SPRTN protease repair histone 3 and topoisomerase 1 DNA-protein crosslinks in vivo. Open Biol 2023; 13:230113. [PMID: 37788708 PMCID: PMC10547559 DOI: 10.1098/rsob.230113] [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: 04/24/2023] [Accepted: 08/14/2023] [Indexed: 10/05/2023] Open
Abstract
DNA-protein crosslinks (DPCs) are frequent and damaging DNA lesions that affect all DNA transactions, which in turn can lead to the formation of double-strand breaks, genomic instability and cell death. At the organismal level, impaired DPC repair (DPCR) is associated with cancer, ageing and neurodegeneration. Despite the severe consequences of DPCs, little is known about the processes underlying repair pathways at the organism level. SPRTN is a protease that removes most cellular DPCs during replication, whereas tyrosyl-DNA phosphodiesterase 1 repairs one of the most abundant enzymatic DPCs, topoisomerase 1-DPC (TOP1-DPC). How these two enzymes repair DPCs at the organism level is currently unknown. We perform phylogenetic, syntenic, structural and expression analysis to compare tyrosyl-DNA phosphodiesterase 1 (TDP1) orthologues between human, mouse and zebrafish. Using the zebrafish animal model and human cells, we demonstrate that TDP1 and SPRTN repair endogenous, camptothecin- and formaldehyde-induced DPCs, including histone H3- and TOP1-DPCs. We show that resolution of H3-DNA crosslinks depends on upstream proteolysis by SPRTN and subsequent peptide removal by TDP1 in RPE1 cells and zebrafish embryos, whereas SPRTN and TDP1 function in different pathways in the repair of endogenous TOP1-DPCs and total DPCs. Furthermore, we have found increased TDP2 expression in TDP1-deficient cells and embryos. Understanding the role of TDP1 in DPCR at the cellular and organismal levels could provide an impetus for the development of new drugs and combination therapies with TOP1-DPC inducing drugs.
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Affiliation(s)
- Ivan Anticevic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Cecile Otten
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Luka Vinkovic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Luka Jukic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Marta Popovic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
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50
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Rosen Y, Brbić M, Roohani Y, Swanson K, Li Z, Leskovec J. Towards Universal Cell Embeddings: Integrating Single-cell RNA-seq Datasets across Species with SATURN. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.03.526939. [PMID: 36778387 PMCID: PMC9915700 DOI: 10.1101/2023.02.03.526939] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, inter-species genomic differences limit the joint analysis of cross-species datasets to homologous genes. Here, we present SATURN, a deep learning method for learning universal cell embeddings that encodes genes' biological properties using protein language models. By coupling protein embeddings from language models with RNA expression, SATURN integrates datasets profiled from different species regardless of their genomic similarity. SATURN has a unique ability to detect functionally related genes co-expressed across species, redefining differential expression for cross-species analysis. We apply SATURN to three species whole-organism atlases and frog and zebrafish embryogenesis datasets. We show that cell embeddings learnt in SATURN can be effectively used to transfer annotations across species and identify both homologous and species-specific cell types, even across evolutionarily remote species. Finally, we use SATURN to reannotate the five species Cell Atlas of Human Trabecular Meshwork and Aqueous Outflow Structures and find evidence of potentially divergent functions between glaucoma associated genes in humans and other species.
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Affiliation(s)
- Yanay Rosen
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Maria Brbić
- School of Computer and Communication Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Yusuf Roohani
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Kyle Swanson
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Ziang Li
- Department of Computer Science and Technology, Tsinghua University, Beijing, China
| | - Jure Leskovec
- Department of Computer Science, Stanford University, Stanford, CA, USA
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