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Losurdo NA, Bibo A, Bedke J, Link N. A novel adipose loss-of-function mutant in Drosophila. Fly (Austin) 2024; 18:2352938. [PMID: 38741287 PMCID: PMC11095658 DOI: 10.1080/19336934.2024.2352938] [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: 08/23/2023] [Accepted: 05/02/2024] [Indexed: 05/16/2024] Open
Abstract
To identify genes required for brain growth, we took an RNAi knockdown reverse genetic approach in Drosophila. One potential candidate isolated from this effort is the anti-lipogenic gene adipose (adp). Adp has an established role in the negative regulation of lipogenesis in the fat body of the fly and adipose tissue in mammals. While fat is key to proper development in general, adp has not been investigated during brain development. Here, we found that RNAi knockdown of adp in neuronal stem cells and neurons results in reduced brain lobe volume and sought to replicate this with a mutant fly. We generated a novel adp mutant that acts as a loss-of-function mutant based on buoyancy assay results. We found that despite a change in fat content in the body overall and a decrease in the number of larger (>5 µm) brain lipid droplets, there was no change in the brain lobe volume of mutant larvae. Overall, our work describes a novel adp mutant that can functionally replace the long-standing adp60 mutant and shows that the adp gene has no obvious involvement in brain growth.
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Affiliation(s)
| | - Adriana Bibo
- Department of Neurobiology, University of Utah, Salt Lake, UT, USA
| | - Jacob Bedke
- Department of Neurobiology, University of Utah, Salt Lake, UT, USA
| | - Nichole Link
- Department of Neurobiology, University of Utah, Salt Lake, UT, USA
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2
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Du L, Liu Q, Wang L, Lyu H, Tang J. Microplastics enhanced the allelopathy of pyrogallol on toxic Microcystis with additional risks: Microcystins release and greenhouse gases emissions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:173864. [PMID: 38879032 DOI: 10.1016/j.scitotenv.2024.173864] [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: 01/21/2024] [Revised: 05/16/2024] [Accepted: 06/07/2024] [Indexed: 06/21/2024]
Abstract
Cyanobacteria blooms (CBs) caused by eutrophication pose a global concern, especially Microcystis aeruginosa (M. aeruginosa), which could release harmful microcystins (MCs). The impact of microplastics (MPs) on allelopathy in freshwater environments is not well understood. This study examined the joint effect of adding polystyrene (PS-MPs) as representative MPs and two concentrations (2 and 8 mg/L) of pyrogallol (PYR) on the allelopathy of M. aeruginosa. The results showed that the addition of PS-MPs intensified the inhibitory effect of 8 mg/L PYR on the growth and photosynthesis of M. aeruginosa. After a 7-day incubation period, the cell density decreased to 69.7 %, and the chl-a content decreased to 48 % compared to the condition without PS-MPs (p < 0.05). Although the growth and photosynthesis of toxic Microcystis decreased with the addition of PS-MPs, the addition of PS-MPs significantly resulted in a 3.49-fold increase in intracellular MCs and a 1.10-fold increase in extracellular MCs (p < 0.05). Additionally, the emission rates of greenhouse gases (GHGs) (carbon dioxide, nitrous oxide and methane) increased by 2.66, 2.23 and 2.17-fold, respectively (p < 0.05). In addition, transcriptomic analysis showed that the addition of PS-MPs led to the dysregulation of gene expression related to DNA synthesis, membrane function, enzyme activity, stimulus detection, MCs release and GHGs emissions in M. aeruginosa. PYR and PS-MPs triggered ROS-induced membrane damage and disrupted photosynthesis in algae, leading to increased MCs and GHG emissions. PS-MPs accumulation exacerbated this issue by impeding light absorption and membrane function, further heightening the release of MCs and GHGs emissions. Therefore, PS-MPs exhibited a synergistic effect with PYR in inhibiting the growth and photosynthesis of M. aeruginosa, resulting in additional risks such as MCs release and GHGs emissions. These results provide valuable insights for the ecological risk assessment and control of algae bloom in freshwater ecosystems.
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Affiliation(s)
- Linqing Du
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Qinglong Liu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Lan Wang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Honghong Lyu
- Tianjin Key Laboratory of Clean Energy and Pollution Control, School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Jingchun Tang
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education)/Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
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3
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Zhu HX, Wright BW, Logel DY, Needham P, Yehl K, Molloy MP, Jaschke PR. IbpAB small heat shock proteins are not host factors for bacteriophage ϕX174 replication. Virology 2024; 597:110169. [PMID: 38996611 DOI: 10.1016/j.virol.2024.110169] [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: 02/01/2024] [Revised: 06/20/2024] [Accepted: 07/02/2024] [Indexed: 07/14/2024]
Abstract
Bacteriophage ϕX174 is a small icosahedral virus of the Microviridae with a rapid replication cycle. Previously, we found that in ϕX174 infections of Escherichia coli, the most highly upregulated host proteins are two small heat shock proteins, IbpA and IbpB, belonging to the HSP20 family, which is a universally conserved group of stress-induced molecular chaperones that prevent irreversible aggregation of proteins. Heat shock proteins were found to protect against ϕX174 lysis, but IbpA/B have not been studied. In this work, we disrupted the ibpA and ibpB genes and measured the effects on ϕX174 replication. We found that in contrast to other E. coli heat shock proteins, they are not necessary for ϕX174 replication; moreover, their absence has no discernible effect on ϕX174 fecundity. These results suggest IbpA/B upregulation is a response to ϕX174 protein expression but does not play a role in phage replication, and they are not Microviridae host factors.
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Affiliation(s)
- Hannah X Zhu
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Bradley W Wright
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Dominic Y Logel
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Patrick Needham
- Miami University, Department of Chemistry and Biochemistry, Oxford, 45056, USA
| | - Kevin Yehl
- Miami University, Department of Chemistry and Biochemistry, Oxford, 45056, USA
| | - Mark P Molloy
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia; Kolling Institute, School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Paul R Jaschke
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia.
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4
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Karkoutly S, Takeuchi Y, Mehrazad Saber Z, Ye C, Tao D, Aita Y, Murayama Y, Shikama A, Masuda Y, Izumida Y, Matsuzaka T, Kawakami Y, Shimano H, Yahagi N. FoxO transcription factors regulate urea cycle through Ass1. Biochem Biophys Res Commun 2024; 739:150594. [PMID: 39191148 DOI: 10.1016/j.bbrc.2024.150594] [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: 08/10/2024] [Revised: 08/14/2024] [Accepted: 08/22/2024] [Indexed: 08/29/2024]
Abstract
When amino acids are plentiful in the diet, the liver upregulates most enzymes responsible for amino acid degradation. In particular, the activity of urea cycle enzymes increases in response to high-protein diets to facilitate the excretion of excess nitrogen. KLF15 has been established as a critical regulator of amino acid catabolism including ureagenesis and we have recently identified FoxO transcription factors as an important upstream regulator of KLF15 in the liver. Therefore, we explored the role of FoxOs in amino acid metabolism under high-protein diet. Our findings revealed that the concentrations of two urea cycle-related amino acids, arginine and ornithine, were significantly altered by FoxOs knockdown. Additionally, using KLF15 knockout mice and an in vivo Ad-luc analytical system, we confirmed that FoxOs directly regulate hepatic Ass1 expression under high-protein intake independently from KLF15. Moreover, ChIP analysis showed that the high-protein diet increased FoxOs DNA binding without altering the nuclear protein amount. Therefore, FoxOs play a direct role in regulating ureagenesis via a KLF15-independent pathway in response to high-protein intake.
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Affiliation(s)
- Samia Karkoutly
- Division of Endocrinology and Metabolism, Department of Medicine, Jichi Medical University, Tochigi, 329-0498, Japan; Nutrigenomics Research Group, Institute of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - Yoshinori Takeuchi
- Division of Endocrinology and Metabolism, Department of Medicine, Jichi Medical University, Tochigi, 329-0498, Japan; Nutrigenomics Research Group, Institute of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - Zahra Mehrazad Saber
- Division of Endocrinology and Metabolism, Department of Medicine, Jichi Medical University, Tochigi, 329-0498, Japan
| | - Chen Ye
- Division of Endocrinology and Metabolism, Department of Medicine, Jichi Medical University, Tochigi, 329-0498, Japan; Nutrigenomics Research Group, Institute of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - Duhan Tao
- Division of Endocrinology and Metabolism, Department of Medicine, Jichi Medical University, Tochigi, 329-0498, Japan; Nutrigenomics Research Group, Institute of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - Yuichi Aita
- Division of Endocrinology and Metabolism, Department of Medicine, Jichi Medical University, Tochigi, 329-0498, Japan; Nutrigenomics Research Group, Institute of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - Yuki Murayama
- Nutrigenomics Research Group, Institute of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan; Department of Internal Medicine (Endocrinology and Metabolism), Institute of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - Akito Shikama
- Nutrigenomics Research Group, Institute of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan; Department of Internal Medicine (Endocrinology and Metabolism), Institute of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - Yukari Masuda
- Division of Endocrinology and Metabolism, Department of Medicine, Jichi Medical University, Tochigi, 329-0498, Japan; Nutrigenomics Research Group, Institute of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - Yoshihiko Izumida
- Nutrigenomics Research Group, Institute of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - Takashi Matsuzaka
- Department of Internal Medicine (Endocrinology and Metabolism), Institute of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - Yasushi Kawakami
- Department of Internal Medicine (Endocrinology and Metabolism), Institute of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - Hitoshi Shimano
- Department of Internal Medicine (Endocrinology and Metabolism), Institute of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - Naoya Yahagi
- Division of Endocrinology and Metabolism, Department of Medicine, Jichi Medical University, Tochigi, 329-0498, Japan; Nutrigenomics Research Group, Institute of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan; Department of Internal Medicine (Endocrinology and Metabolism), Institute of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan.
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5
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Alvarado K, Tang WJ, Watson CJ, Ahmed AR, Gomez AE, Donaka R, Amemiya C, Karasik D, Hsu YH, Kwon RY. Loss of cped1 does not affect bone and lean tissue in zebrafish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.601974. [PMID: 39026892 PMCID: PMC11257572 DOI: 10.1101/2024.07.10.601974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Human genetic studies have nominated Cadherin-like and PC-esterase Domain-containing 1 (CPED1) as a candidate target gene mediating bone mineral density (BMD) and fracture risk heritability. Recent efforts to define the role of CPED1 in bone in mouse and human models have revealed complex alternative splicing and inconsistent results arising from gene targeting, making its function in bone difficult to interpret. To better understand the role of CPED1 in adult bone mass and morphology, we conducted a comprehensive genetic and phenotypic analysis of cped1 in zebrafish, an emerging model for bone and mineral research. We analyzed two different cped1 mutant lines and performed deep phenotyping to characterize more than 200 measures of adult vertebral, craniofacial, and lean tissue morphology. We also examined alternative splicing of zebrafish cped1 and gene expression in various cell/tissue types. Our studies fail to support an essential role of cped1 in adult zebrafish bone. Specifically, homozygous mutants for both cped1 mutant alleles, which are expected to result in loss-of-function and impact all cped1 isoforms, exhibited no significant differences in the measures examined when compared to their respective wildtype controls, suggesting that cped1 does not significantly contribute to these traits. We identified sequence differences in critical residues of the catalytic triad between the zebrafish and mouse orthologs of CPED1, suggesting that differences in key residues, as well as distinct alternative splicing, could underlie different functions of CPED1 orthologs in the two species. Our studies fail to support a requirement of cped1 in zebrafish bone and lean tissue, adding to evidence that variants at 7q31.31 can act independently of CPED1 to influence BMD and fracture risk.
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Affiliation(s)
- Kurtis Alvarado
- Department of Orthopaedic Surgery and Sports Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - W. Joyce Tang
- Department of Orthopaedic Surgery and Sports Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Claire J. Watson
- Department of Orthopaedic Surgery and Sports Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Ali R. Ahmed
- Department of Orthopaedic Surgery and Sports Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Arianna Ericka Gomez
- Department of Orthopaedic Surgery and Sports Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | | | - Chris Amemiya
- Department of Molecular and Cell Biology and Quantitative and Systems Biology Program, University of California, Merced, CA, USA
| | - David Karasik
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Hebrew SeniorLife, Hinda and Arthur Marcus Institute for Aging Research, Boston, MA, USA
| | - Yi-Hsiang Hsu
- Hebrew SeniorLife, Hinda and Arthur Marcus Institute for Aging Research, Boston, MA, USA
| | - Ronald Young Kwon
- Department of Orthopaedic Surgery and Sports Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
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6
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Zhakula-Kostadinova N, Taylor AM. Patterns of Aneuploidy and Signaling Consequences in Cancer. Cancer Res 2024; 84:2575-2587. [PMID: 38924459 PMCID: PMC11325152 DOI: 10.1158/0008-5472.can-24-0169] [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: 01/16/2024] [Revised: 03/29/2024] [Accepted: 06/20/2024] [Indexed: 06/28/2024]
Abstract
Aneuploidy, or a change in the number of whole chromosomes or chromosome arms, is a near-universal feature of cancer. Chromosomes affected by aneuploidy are not random, with observed cancer-specific and tissue-specific patterns. Recent advances in genome engineering methods have allowed the creation of models with targeted aneuploidy events. These models can be used to uncover the downstream effects of individual aneuploidies on cancer phenotypes including proliferation, apoptosis, metabolism, and immune signaling. Here, we review the current state of research into the patterns of aneuploidy in cancer and their impact on signaling pathways and biological processes.
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Affiliation(s)
- Nadja Zhakula-Kostadinova
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Alison M Taylor
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
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7
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Mellis IA, Melzer ME, Bodkin N, Goyal Y. Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells. Genome Biol 2024; 25:217. [PMID: 39135102 PMCID: PMC11320884 DOI: 10.1186/s13059-024-03351-2] [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: 12/13/2023] [Accepted: 07/25/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND Cells and tissues have a remarkable ability to adapt to genetic perturbations via a variety of molecular mechanisms. Nonsense-induced transcriptional compensation, a form of transcriptional adaptation, has recently emerged as one such mechanism, in which nonsense mutations in a gene trigger upregulation of related genes, possibly conferring robustness at cellular and organismal levels. However, beyond a handful of developmental contexts and curated sets of genes, no comprehensive genome-wide investigation of this behavior has been undertaken for mammalian cell types and conditions. How the regulatory-level effects of inherently stochastic compensatory gene networks contribute to phenotypic penetrance in single cells remains unclear. RESULTS We analyze existing bulk and single-cell transcriptomic datasets to uncover the prevalence of transcriptional adaptation in mammalian systems across diverse contexts and cell types. We perform regulon gene expression analyses of transcription factor target sets in both bulk and pooled single-cell genetic perturbation datasets. Our results reveal greater robustness in expression of regulons of transcription factors exhibiting transcriptional adaptation compared to those of transcription factors that do not. Stochastic mathematical modeling of minimal compensatory gene networks qualitatively recapitulates several aspects of transcriptional adaptation, including paralog upregulation and robustness to mutation. Combined with machine learning analysis of network features of interest, our framework offers potential explanations for which regulatory steps are most important for transcriptional adaptation. CONCLUSIONS Our integrative approach identifies several putative hits-genes demonstrating possible transcriptional adaptation-to follow-up on experimentally and provides a formal quantitative framework to test and refine models of transcriptional adaptation.
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Affiliation(s)
- Ian A Mellis
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
| | - Madeline E Melzer
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Nicholas Bodkin
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- CZ Biohub Chicago, LLC, Chicago, IL, USA.
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8
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Kiran Kumar KD, Singh S, Schmelzle SM, Vogel P, Fruhner C, Hanswillemenke A, Brun A, Wettengel J, Füll Y, Funk L, Mast V, Botsch JJ, Reautschnig P, Li JB, Stafforst T. An improved SNAP-ADAR tool enables efficient RNA base editing to interfere with post-translational protein modification. Nat Commun 2024; 15:6615. [PMID: 39103360 DOI: 10.1038/s41467-024-50395-w] [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: 09/26/2023] [Accepted: 07/09/2024] [Indexed: 08/07/2024] Open
Abstract
RNA base editing relies on the introduction of adenosine-to-inosine changes into target RNAs in a highly programmable manner in order to repair disease-causing mutations. Here, we propose that RNA base editing could be broadly applied to perturb protein function by removal of regulatory phosphorylation and acetylation sites. We demonstrate the feasibility on more than 70 sites in various signaling proteins and identify key determinants for high editing efficiency and potent down-stream effects. For the JAK/STAT pathway, we demonstrate both, negative and positive regulation. To achieve high editing efficiency over a broad codon scope, we applied an improved version of the SNAP-ADAR tool. The transient nature of RNA base editing enables the comparably fast (hours to days), dose-dependent (thus partial) and reversible manipulation of regulatory sites, which is a key advantage over DNA (base) editing approaches. In summary, PTM interference might become a valuable field of application of RNA base editing.
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Affiliation(s)
| | - Shubhangi Singh
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | | | - Paul Vogel
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Carolin Fruhner
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | | | - Adrian Brun
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Jacqueline Wettengel
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Yvonne Füll
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Lukas Funk
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Valentin Mast
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - J Josephine Botsch
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Philipp Reautschnig
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Thorsten Stafforst
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.
- Gene and RNA Therapy Center (GRTC), Faculty of Medicine University Tübingen, Tübingen, Germany.
- iFIT Cluster of Excellence (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies, University of Tübingen, Tübingen, Germany.
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9
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Hur KH, Lee Y, Donio AL, Kim SK, Lee BR, Seo JY, Kundu D, Kim KM, Kohut SJ, Lee SY, Jang CG. Transient receptor potential ankyrin 1 channel modulates the abuse-related mechanisms of methamphetamine through interaction with dopamine transporter. Br J Pharmacol 2024; 181:2794-2809. [PMID: 38644533 PMCID: PMC11230846 DOI: 10.1111/bph.16370] [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: 09/07/2023] [Revised: 02/17/2024] [Accepted: 02/29/2024] [Indexed: 04/23/2024] Open
Abstract
BACKGROUND AND PURPOSE Methamphetamine (METH) use disorder has risen dramatically over the past decade, and there are currently no FDA-approved medications due, in part, to gaps in our understanding of the pharmacological mechanisms related to METH action in the brain. EXPERIMENTAL APPROACH Here, we investigated whether transient receptor potential ankyrin 1 (TRPA1) mediates each of several METH abuse-related behaviours in rodents: self-administration, drug-primed reinstatement, acquisition of conditioned place preference, and hyperlocomotion. Additionally, METH-induced molecular (i.e., neurotransmitter and protein) changes in the brain were compared between wild-type and TRPA1 knock-out mice. Finally, the relationship between TRPA1 and the dopamine transporter was investigated through immunoprecipitation and dopamine reuptake assays. KEY RESULTS TRPA1 antagonism blunted METH self-administration and drug-primed reinstatement of METH-seeking behaviour. Further, development of METH-induced conditioned place preference and hyperlocomotion were inhibited by TRPA1 antagonist treatment, effects that were not observed in TRPA1 knock-out mice. Similarly, molecular studies revealed METH-induced increases in dopamine levels and expression of dopamine system-related proteins in wild-type, but not in TRPA1 knock-out mice. Furthermore, pharmacological blockade of TRPA1 receptors reduced the interaction between TRPA1 and the dopamine transporter, thereby increasing dopamine reuptake activity by the transporter. CONCLUSION AND IMPLICATIONS This study demonstrates that TRPA1 is involved in the abuse-related behavioural effects of METH, potentially through its modulatory role in METH-induced activation of dopaminergic neurotransmission. Taken together, these data suggest that TRPA1 may be a novel therapeutic target for treating METH use disorder.
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Affiliation(s)
- Kwang-Hyun Hur
- Department of Pharmacology, School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
- Behavioral Neuroimaging Laboratory, McLean Hospital, Boston, Massachusetts, USA
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, USA
| | - Youyoung Lee
- Department of Pharmacology, School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Audrey Lynn Donio
- Department of Pharmacology, School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Seon-Kyung Kim
- Department of Pharmacology, School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Bo-Ram Lee
- Department of Pharmacology, School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jee-Yeon Seo
- Department of Pharmacology, School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Dooti Kundu
- Department of Pharmacology, College of Pharmacy, Chonnam National University, Gwang-Ju, Republic of Korea
| | - Kyeong-Man Kim
- Department of Pharmacology, College of Pharmacy, Chonnam National University, Gwang-Ju, Republic of Korea
| | - Stephen J Kohut
- Behavioral Neuroimaging Laboratory, McLean Hospital, Boston, Massachusetts, USA
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, USA
| | - Seok-Yong Lee
- Department of Pharmacology, School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Choon-Gon Jang
- Department of Pharmacology, School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
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10
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Wang C, Xie Q, Xia X, Zhang C, Jiang S, Wang S, Zhang X, Hua R, Xue J, Zheng H. ZMYND12 serves as an IDAd subunit that is essential for sperm motility in mice. Cell Mol Life Sci 2024; 81:317. [PMID: 39066891 PMCID: PMC11335240 DOI: 10.1007/s00018-024-05344-7] [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: 12/13/2023] [Revised: 06/04/2024] [Accepted: 07/01/2024] [Indexed: 07/30/2024]
Abstract
Inner dynein arms (IDAs) are formed from a protein complex that is essential for appropriate flagellar bending and beating. IDA defects have previously been linked to the incidence of asthenozoospermia (AZS) and male infertility. The testes-enriched ZMYND12 protein is homologous with an IDA component identified in Chlamydomonas. ZMYND12 deficiency has previously been tied to infertility in males, yet the underlying mechanism remains uncertain. Here, a CRISPR/Cas9 approach was employed to generate Zmynd12 knockout (Zmynd12-/-) mice. These Zmynd12-/- mice exhibited significant male subfertility, reduced sperm motile velocity, and impaired capacitation. Through a combination of co-immunoprecipitation and mass spectrometry, ZMYND12 was found to interact with TTC29 and PRKACA. Decreases in the levels of PRKACA were evident in the sperm of these Zmynd12-/- mice, suggesting that this change may account for the observed drop in male fertility. Moreover, in a cohort of patients with AZS, one patient carrying a ZMYND12 variant was identified, expanding the known AZS-related variant spectrum. Together, these findings demonstrate that ZMYND12 is essential for flagellar beating, capacitation, and male fertility.
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Affiliation(s)
- Chang Wang
- College of Nursing, Anhui University of Chinese Medicine, Hefei, Anhui, 230012, China
| | - Qingsong Xie
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui, 230032, China
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, Anhui, 230032, China
| | - Xun Xia
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui, 230032, China
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, Anhui, 230032, China
| | - Chuanying Zhang
- College of Nursing, Anhui University of Chinese Medicine, Hefei, Anhui, 230012, China
| | - Shan Jiang
- College of Nursing, Anhui University of Chinese Medicine, Hefei, Anhui, 230012, China
| | - Sihan Wang
- College of Nursing, Anhui University of Chinese Medicine, Hefei, Anhui, 230012, China
| | - Xi Zhang
- Department of Reproductive Health and Infertility Clinic, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu, 223300, China
| | - Rong Hua
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, China.
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui, 230032, China.
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, Anhui, 230032, China.
| | - Jiangyang Xue
- The Central Laboratory of Birth Defects Prevention and Control, Ningbo Key Laboratory for the Prevention and Treatment of Embryogenic Diseases, Women and Children's Hospital of Ningbo University, Ningbo, Zhejiang, 315000, China.
| | - Haoyu Zheng
- Department of Gynaecology, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu, 223300, China.
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11
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LaCoursiere CM, Ullmann JF, Koh HY, Turner L, Baker CM, Robens B, Shao W, Rotenberg A, McGraw CM, Poduri AH. Zebrafish models of candidate human epilepsy-associated genes provide evidence of hyperexcitability. iScience 2024; 27:110172. [PMID: 39021799 PMCID: PMC11253282 DOI: 10.1016/j.isci.2024.110172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/13/2024] [Accepted: 05/31/2024] [Indexed: 07/20/2024] Open
Abstract
Hundreds of novel candidate human epilepsy-associated genes have been identified thanks to advancements in next-generation sequencing and large genome-wide association studies, but establishing genetic etiology requires functional validation. We generated a list of >2,200 candidate epilepsy-associated genes, of which 48 were developed into stable loss-of-function (LOF) zebrafish models. Of those 48, evidence of seizure-like behavior was present in 5 (arfgef1, kcnd2, kcnv1, ubr5, and wnt8b). Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally, arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further, RNA sequencing (RNA-seq) revealed convergent transcriptional abnormalities between mutant lines, consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1, KCND2, and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.
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Affiliation(s)
- Christopher Mark LaCoursiere
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children’s Hospital, Boston, MA 02115, USA
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Jeremy F.P. Ullmann
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children’s Hospital, Boston, MA 02115, USA
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Hyun Yong Koh
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children’s Hospital, Boston, MA 02115, USA
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA 02115, USA
- Departments of Neuroscience and Pediatrics, Division of Neurology and Developmental Neuroscience, BCM, Houston, TX 77030, USA
| | - Laura Turner
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children’s Hospital, Boston, MA 02115, USA
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Cristina M. Baker
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children’s Hospital, Boston, MA 02115, USA
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA 02115, USA
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, 7034 Trondheim, Norway
| | - Barbara Robens
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children’s Hospital, Boston, MA 02115, USA
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Wanqing Shao
- Research Computing, Department of Information Technology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Alexander Rotenberg
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Christopher M. McGraw
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children’s Hospital, Boston, MA 02115, USA
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Annapurna H. Poduri
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children’s Hospital, Boston, MA 02115, USA
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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12
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Yin E, Esbin MN. Optimized CRISPR-based knockout in BeWo cells. Placenta 2024:S0143-4004(24)00300-X. [PMID: 38997889 DOI: 10.1016/j.placenta.2024.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 07/14/2024]
Abstract
CRISPR genome editing is a widely used tool to perturb genes of interest within cells and tissues and can be used as a research tool to study the connection between genotypes and cellular phenotypes. Highly efficient genome editing is limited in certain cell types due to low transfection efficiency or single-cell survivability. This is true for BeWo cells, an in vitro model of placental syncytiotrophoblast cell-cell fusion and hormone secretion. Here we describe an optimized and easy-to-use protocol for knockout in BeWo cells using CRISPR Cas9 ribonucleoprotein (RNP) complexes delivered via electroporation. Further, we describe parameters for successful guide RNA design and how to assess genetic knockouts in BeWo cells so that users can apply this technique to their own genes of interest. We provide a positive control for inducing highly efficient knockout of the cell-cell fusion protein Syncytin-2 (ERVFRD-1) and assessing editing efficiency at this locus. We anticipate that efficient RNP-mediated genetic knockouts in BeWo cells will facilitate the study of new genes involved in cell-cell fusion and hormone secretion in this important cellular model system. Furthermore, this strategy of optimized nucleofection and RNP delivery may be of use in other difficult-to-edit trophoblast cells or could be applied to efficiently deliver transgenes to BeWo cells.
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Affiliation(s)
- Eric Yin
- University of California, Berkeley, United States
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13
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Sannes AC, Ghani U, Niazi IK, Moberget T, Jonassen R, Haavik H, Gjerstad J. Investigating Whether a Combination of Electro-Encephalography and Gene Expression Profiling Can Predict the Risk of Chronic Pain: A Protocol for an Observational Prospective Cohort Study. Brain Sci 2024; 14:641. [PMID: 39061381 PMCID: PMC11274615 DOI: 10.3390/brainsci14070641] [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: 05/07/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
Despite most episodes of low back pain (LBP) being short-lasting, some transition into persistent long-lasting problems. Hence, the need for a deeper understanding of the physiological mechanisms of this is pertinent. Therefore, the aims of the present study are (1) to map pain-induced changes in brain activity and blood gene expression associated with persistent LBP, and (2) to explore whether these brain and gene expression signatures show promise as predictive biomarkers for the development of persistent LBP. The participants will be allocated into three different pain groups (no pain, mild short-lasting, or moderate long-term). One in-person visit, where two blood samples will be collected and sent for RNA sequencing, along with resting 64-channel electro-encephalography measurements before, during, and after a cold pressor test, will be conducted. Thereafter, follow-up questionnaires will be distributed at 2 weeks, 3 months, and 6 months. Recruitment will start during the second quarter of 2024, with expected completion by the last quarter of 2024. The results are expected to provide insight into the relationship between central nervous system activity, gene expression profiles, and LBP. If successful, this study has the potential to provide physiological indicators that are sensitive to the transition from mild, short-term LBP to more problematic, long-term LBP.
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Affiliation(s)
- Ann-Christin Sannes
- Faculty of Health Science, Oslo Metropolitan University, 0890 Oslo, Norway
- Department for Research and Development in Mental Health, Akershus University Hospital, 1474 Lørenskog, Norway
| | - Usman Ghani
- Centre for Chiropractic Research, New Zealand College of Chiropractic, Auckland 1060, New Zealand (I.K.N.)
- Faculty of Health & Environmental Sciences, Health & Rehabilitation Research Institute, AUT University, Auckland 1010, New Zealand
| | - Imran Khan Niazi
- Centre for Chiropractic Research, New Zealand College of Chiropractic, Auckland 1060, New Zealand (I.K.N.)
- Faculty of Health & Environmental Sciences, Health & Rehabilitation Research Institute, AUT University, Auckland 1010, New Zealand
- Faculty of Medicine, Aalborg University, 9260 Aalborg, Denmark
| | - Torgeir Moberget
- Faculty of Health Sciences, Kristiania University College, 0107 Oslo, Norway
- Centre for Precision Psychiatry, University of Oslo, 0373 Oslo, Norway
| | - Rune Jonassen
- Faculty of Health Science, Oslo Metropolitan University, 0890 Oslo, Norway
| | - Heidi Haavik
- Centre for Chiropractic Research, New Zealand College of Chiropractic, Auckland 1060, New Zealand (I.K.N.)
| | - Johannes Gjerstad
- Department for Research and Development in Mental Health, Akershus University Hospital, 1474 Lørenskog, Norway
- Faculty of Health Sciences, Kristiania University College, 0107 Oslo, Norway
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14
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Dominguez-Ortiz J, Álvarez-Gómez RM, Montiel-Manríquez R, Cedro-Tanda A, Alcaraz N, Castro-Hernández C, Bautista-Hinojosa L, Contreras-Espinosa L, Torres-Maldonado L, Fragoso-Ontiveros V, Sánchez-Contreras Y, González-Barrios R, la Fuente-Hernández MAD, Mejía-Aguayo MDLL, Juárez-Figueroa U, Padua-Bracho A, Sosa-León R, Obregon-Serrano G, Vidal-Millán S, Núñez-Martínez PM, Pedroza-Torres A, Nicasio-Arzeta S, Rodríguez A, Luna F, Cisneros-Soberanis F, Frías S, Arriaga-Canon C, Herrera-Montalvo LA. A Molecular Characterization of the Allelic Expression of the BRCA1 Founder Δ9-12 Pathogenic Variant and Its Potential Clinical Relevance in Hereditary Cancer. Int J Mol Sci 2024; 25:6773. [PMID: 38928478 PMCID: PMC11204022 DOI: 10.3390/ijms25126773] [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: 04/25/2024] [Revised: 06/13/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024] Open
Abstract
Hereditary breast and ovarian cancer (HBOC) syndrome is a genetic condition that increases the risk of breast cancer by 80% and that of ovarian cancer by 40%. The most common pathogenic variants (PVs) causing HBOC occur in the BRCA1 gene, with more than 3850 reported mutations in the gene sequence. The prevalence of specific PVs in BRCA1 has increased across populations due to the effect of founder mutations. Therefore, when a founder mutation is identified, it becomes key to improving cancer risk characterization and effective screening protocols. The only founder mutation described in the Mexican population is the deletion of exons 9 to 12 of BRCA1 (BRCA1Δ9-12), and its description focuses on the gene sequence, but no transcription profiles have been generated for individuals who carry this gene. In this study, we describe the transcription profiles of cancer patients and healthy individuals who were heterozygous for PV BRCA1Δ9-12 by analyzing the differential expression of both alleles compared with the homozygous BRCA1 control group using RT-qPCR, and we describe the isoforms produced by the BRCA1 wild-type and BRCA1Δ9-12 alleles using nanopore long-sequencing. Using the Kruskal-Wallis test, our results showed a similar transcript expression of the wild-type allele between the healthy heterozygous group and the homozygous BRCA1 control group. An association between the recurrence and increased expression of both alleles in HBOC patients was also observed. An analysis of the sequences indicated four wild-type isoforms with diagnostic potential for discerning individuals who carry the PV BRCA1Δ9-12 and identifying which of them has developed cancer.
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Affiliation(s)
- Julieta Dominguez-Ortiz
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (J.D.-O.); (R.M.-M.); (C.C.-H.); (L.B.-H.); (L.C.-E.); (R.G.-B.); (F.L.)
- Instituto Nacional de Cancerología, Universidad Nacional Autónoma de México (UNAM), Coyoacán, Mexico City 04510, Mexico
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Rosa M. Álvarez-Gómez
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Rogelio Montiel-Manríquez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (J.D.-O.); (R.M.-M.); (C.C.-H.); (L.B.-H.); (L.C.-E.); (R.G.-B.); (F.L.)
| | - Alberto Cedro-Tanda
- Núcleo B de Innovación en Medicina de Precisión, Instituto Nacional de Medicina Genómica, Periférico Sur 4809, Arenal Tepepan, Tlalpan, Mexico City 14610, Mexico;
| | - Nicolás Alcaraz
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3A, 2200 Copenhagen, Denmark;
| | - Clementina Castro-Hernández
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (J.D.-O.); (R.M.-M.); (C.C.-H.); (L.B.-H.); (L.C.-E.); (R.G.-B.); (F.L.)
| | - Luis Bautista-Hinojosa
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (J.D.-O.); (R.M.-M.); (C.C.-H.); (L.B.-H.); (L.C.-E.); (R.G.-B.); (F.L.)
| | - Laura Contreras-Espinosa
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (J.D.-O.); (R.M.-M.); (C.C.-H.); (L.B.-H.); (L.C.-E.); (R.G.-B.); (F.L.)
| | - Leda Torres-Maldonado
- Instituto Nacional de Pediatría, Insurgentes Sur No. 3700-C. Coyoacán, Mexico City 04530, Mexico; (L.T.-M.); (U.J.-F.); (A.R.); (S.F.)
| | - Verónica Fragoso-Ontiveros
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Yuliana Sánchez-Contreras
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Rodrigo González-Barrios
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (J.D.-O.); (R.M.-M.); (C.C.-H.); (L.B.-H.); (L.C.-E.); (R.G.-B.); (F.L.)
| | - Marcela Angélica De la Fuente-Hernández
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - María de la Luz Mejía-Aguayo
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Ulises Juárez-Figueroa
- Instituto Nacional de Pediatría, Insurgentes Sur No. 3700-C. Coyoacán, Mexico City 04530, Mexico; (L.T.-M.); (U.J.-F.); (A.R.); (S.F.)
| | - Alejandra Padua-Bracho
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Rodrigo Sosa-León
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Gabriela Obregon-Serrano
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Silvia Vidal-Millán
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Paulina María Núñez-Martínez
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Abraham Pedroza-Torres
- Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología, Av. San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (R.M.Á.-G.); (V.F.-O.); (Y.S.-C.); (M.A.D.l.F.-H.); (M.d.l.L.M.-A.); (A.P.-B.); (R.S.-L.); (G.O.-S.); (S.V.-M.); (P.M.N.-M.); (A.P.-T.)
| | - Sergio Nicasio-Arzeta
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO 80521, USA;
| | - Alfredo Rodríguez
- Instituto Nacional de Pediatría, Insurgentes Sur No. 3700-C. Coyoacán, Mexico City 04530, Mexico; (L.T.-M.); (U.J.-F.); (A.R.); (S.F.)
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), México City 04510, Mexico
| | - Fernando Luna
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (J.D.-O.); (R.M.-M.); (C.C.-H.); (L.B.-H.); (L.C.-E.); (R.G.-B.); (F.L.)
| | - Fernanda Cisneros-Soberanis
- Wellcome Trust Centre for Cell Biology, ICB, University of Edinburgh, Michael Swann Building, King’s Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK;
| | - Sara Frías
- Instituto Nacional de Pediatría, Insurgentes Sur No. 3700-C. Coyoacán, Mexico City 04530, Mexico; (L.T.-M.); (U.J.-F.); (A.R.); (S.F.)
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), México City 04510, Mexico
| | - Cristian Arriaga-Canon
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (J.D.-O.); (R.M.-M.); (C.C.-H.); (L.B.-H.); (L.C.-E.); (R.G.-B.); (F.L.)
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey 64710, Mexico
| | - Luis A. Herrera-Montalvo
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City 14080, Mexico; (J.D.-O.); (R.M.-M.); (C.C.-H.); (L.B.-H.); (L.C.-E.); (R.G.-B.); (F.L.)
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey 64710, Mexico
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15
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Su T, Liu H, Wu Y, Wang J, He F, Li H, Li S, Wang L, Li L, Cao J, Lu Q, Zhao X, Xiang H, Lin C, Lu S, Liu B, Kong F, Fang C. Soybean hypocotyl elongation is regulated by a MYB33-SWEET11/21-GA2ox8c module involving long-distance sucrose transport. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38861663 DOI: 10.1111/pbi.14409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/01/2024] [Accepted: 05/27/2024] [Indexed: 06/13/2024]
Abstract
The length of hypocotyl affects the height of soybean and lodging resistance, thus determining the final grain yield. However, research on soybean hypocotyl length is scarce, and the regulatory mechanisms are not fully understood. Here, we identified a module controlling the transport of sucrose, where sucrose acts as a messenger moved from cotyledon to hypocotyl, regulating hypocotyl elongation. This module comprises four key genes, namely MYB33, SWEET11, SWEET21 and GA2ox8c in soybean. In cotyledon, MYB33 is responsive to sucrose and promotes the expression of SWEET11 and SWEET21, thereby facilitating sucrose transport from the cotyledon to the hypocotyl. Subsequently, sucrose transported from the cotyledon up-regulates the expression of GA2ox8c in the hypocotyl, which ultimately affects the length of the hypocotyl. During the domestication and improvement of soybean, an allele of MYB33 with enhanced abilities to promote SWEET11 and SWEET21 has gradually become enriched in landraces and cultivated varieties, SWEET11 and SWEET21 exhibit high conservation and have undergone a strong purified selection and GA2ox8c is under a strong artificial selection. Our findings identify a new molecular pathway in controlling soybean hypocotyl elongation and provide new insights into the molecular mechanism of sugar transport in soybean.
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Affiliation(s)
- Tong Su
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Huan Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yichun Wu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Jianhao Wang
- Vegetables Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, China
| | - Fanglei He
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
- Institute of Improvement and Utilization of Characteristic Resource Plants, College of Agriculture and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Haiyang Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Shichen Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Lingshuang Wang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Lanxin Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Jie Cao
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Qiulian Lu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xiaohui Zhao
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Hongtao Xiang
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Suihua Branch, Heilongjiang Academy of Agricultural Machinery Sciences, Suihua, China
| | - Chun Lin
- Institute of Improvement and Utilization of Characteristic Resource Plants, College of Agriculture and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Sijia Lu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, China
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16
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Zimmer AM. Ammonia excretion by the fish gill: discoveries and ideas that shaped our current understanding. J Comp Physiol B 2024:10.1007/s00360-024-01561-5. [PMID: 38849577 DOI: 10.1007/s00360-024-01561-5] [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: 12/15/2023] [Revised: 03/06/2024] [Accepted: 05/15/2024] [Indexed: 06/09/2024]
Abstract
The fish gill serves many physiological functions, among which is the excretion of ammonia, the primary nitrogenous waste in most fishes. Although it is the end-product of nitrogen metabolism, ammonia serves many physiological functions including acting as an acid equivalent and as a counter-ion in mechanisms of ion regulation. Our current understanding of the mechanisms of ammonia excretion have been influenced by classic experimental work, clever mechanistic approaches, and modern molecular and genetic techniques. In this review, I will overview the history of the study of ammonia excretion by the gills of fishes, highlighting the important advancements that have shaped this field with a nearly 100-year history. The developmental and evolutionary implications of an ammonia and gill-dominated nitrogen regulation strategy in most fishes will also be discussed. Throughout the review, I point to areas in which more work is needed to push forward this field of research that continues to produce novel insights and discoveries that will undoubtedly shape our overall understanding of fish physiology.
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Affiliation(s)
- Alex M Zimmer
- Department of Biological Sciences, University of New Brunswick, 100 Tucker Park Road, Saint John, Saint John, New Brunswick, E2L 4L5, Canada.
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17
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Marshall GF, Fasol M, Davies FCJ, Le Seelleur M, Fernandez Alvarez A, Bennett-Ness C, Gonzalez-Sulser A, Abbott CM. Face-valid phenotypes in a mouse model of the most common mutation in EEF1A2-related neurodevelopmental disorder. Dis Model Mech 2024; 17:dmm050501. [PMID: 38179821 PMCID: PMC10855229 DOI: 10.1242/dmm.050501] [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: 09/07/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
De novo heterozygous missense mutations in EEF1A2, encoding neuromuscular translation-elongation factor eEF1A2, are associated with developmental and epileptic encephalopathies. We used CRISPR/Cas9 to recapitulate the most common mutation, E122K, in mice. Although E122K heterozygotes were not observed to have convulsive seizures, they exhibited frequent electrographic seizures and EEG abnormalities, transient early motor deficits and growth defects. Both E122K homozygotes and Eef1a2-null mice developed progressive motor abnormalities, with E122K homozygotes reaching humane endpoints by P31. The null phenotype is driven by progressive spinal neurodegeneration; however, no signs of neurodegeneration were observed in E122K homozygotes. The E122K protein was relatively stable in neurons yet highly unstable in skeletal myocytes, suggesting that the E122K/E122K phenotype is instead driven by loss of function in muscle. Nevertheless, motor abnormalities emerged far earlier in E122K homozygotes than in nulls, suggesting a toxic gain of function and/or a possible dominant-negative effect. This mouse model represents the first animal model of an EEF1A2 missense mutation with face-valid phenotypes and has provided mechanistic insights needed to inform rational treatment design.
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Affiliation(s)
- Grant F. Marshall
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Melissa Fasol
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH8 9XD, UK
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Faith C. J. Davies
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Matthew Le Seelleur
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Alejandra Fernandez Alvarez
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Cavan Bennett-Ness
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Alfredo Gonzalez-Sulser
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH8 9XD, UK
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Catherine M. Abbott
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH8 9XD, UK
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18
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Seo MG, Lim Y, Hendelman A, Robitaille G, Beak HK, Hong WJ, Park SJ, Lippman ZB, Park YJ, Kwon CT. Evolutionary conservation of receptor compensation for stem cell homeostasis in Solanaceae plants. HORTICULTURE RESEARCH 2024; 11:uhae126. [PMID: 38919555 PMCID: PMC11197305 DOI: 10.1093/hr/uhae126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 04/21/2024] [Indexed: 06/27/2024]
Abstract
Stem cell homeostasis is pivotal for continuous and programmed formation of organs in plants. The precise control of meristem proliferation is mediated by the evolutionarily conserved signaling that encompasses complex interactions among multiple peptide ligands and their receptor-like kinases. Here, we identified compensation mechanisms involving the CLAVATA1 (CLV1) receptor and its paralogs, BARELY ANY MERISTEMs (BAMs), for stem cell proliferation in two Solanaceae species, tomato and groundcherry. Genetic analyses of higher-order mutants deficient in multiple receptor genes, generated via CRISPR-Cas9 genome editing, reveal that tomato SlBAM1 and SlBAM2 compensate for slclv1 mutations. Unlike the compensatory responses between orthologous receptors observed in Arabidopsis, tomato slclv1 mutations do not trigger transcriptional upregulation of four SlBAM genes. The compensation mechanisms within receptors are also conserved in groundcherry, and critical amino acid residues of the receptors associated with the physical interaction with peptide ligands are highly conserved in Solanaceae plants. Our findings demonstrate that the evolutionary conservation of both compensation mechanisms and critical coding sequences between receptor-like kinases provides a strong buffering capacity during stem cell homeostasis in tomato and groundcherry.
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Affiliation(s)
- Myeong-Gyun Seo
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Yoonseo Lim
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Gina Robitaille
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Hong Kwan Beak
- Division of Biological Sciences and Research Institute for Basic Science, Wonkwang University, Iksan, Jeonbuk 54538, Republic of Korea
| | - Woo-Jong Hong
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Soon Ju Park
- Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Young-Joon Park
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Choon-Tak Kwon
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin 17104, Republic of Korea
- Department of Smart Farm Science, Kyung Hee University, Yongin 17104, Republic of Korea
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19
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Nobili S, Micheli L, Lucarini E, Toti A, Ghelardini C, Di Cesare Mannelli L. Ultramicronized N-palmitoylethanolamine associated with analgesics: Effects against persistent pain. Pharmacol Ther 2024; 258:108649. [PMID: 38615798 DOI: 10.1016/j.pharmthera.2024.108649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 03/27/2024] [Accepted: 04/02/2024] [Indexed: 04/16/2024]
Abstract
Current epidemiological data estimate that one in five people suffers from chronic pain with considerable impairment of health-related quality of life. The pharmacological treatment is based on first- and second-line analgesic drugs, including COX-2 selective and nonselective nonsteroidal anti-inflammatory drugs, paracetamol, antidepressants, anti-seizure drugs and opioids, that are characterized by important side effects. N-palmitoylethanolamine (PEA) is a body's own fatty-acid ethanolamide belonging to the family of autacoid local injury antagonist amides. The anti-inflammatory and pain-relieving properties of PEA have been recognized for decades and prompted to depict its role in the endogenous mechanisms of pain control. Together with its relative abundance in food sources, this opened the way to the use of PEA as a pain-relieving nutritional intervention. Naïve PEA is a large particle size lipid molecule with low solubility and bioavailability. Reducing particle size is a useful method to increase surface area, thereby improving dissolution rate and bioavailability accordingly. Micron-size formulations of PEA (e.g., ultramicronized and co-(ultra)micronized) have shown higher oral efficacy compared to naïve PEA. In particular, ultramicronized PEA has been shown to efficiently cross the intestinal wall and, more importantly, the blood-brain and blood-spinal cord barrier. Several preclinical and clinical studies have shown the efficacy, safety and tolerability of ultramicronized PEA. This narrative review summarizes the available pharmacokinetic/pharmacodynamic data on ultramicronized PEA and focuses to its contribution to pain control, in particular as 'add-on' nutritional intervention. Data showing the ability of ultramicronized PEA to limit opioid side effects, including the development of tolerance, have also been reviewed.
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Affiliation(s)
- Stefania Nobili
- Department of Neuroscience, Psychology, Drug Research and Child Health - NEUROFARBA - Pharmacology and Toxicology Section, University of Florence, Florence, Italy.
| | - Laura Micheli
- Department of Neuroscience, Psychology, Drug Research and Child Health - NEUROFARBA - Pharmacology and Toxicology Section, University of Florence, Florence, Italy
| | - Elena Lucarini
- Department of Neuroscience, Psychology, Drug Research and Child Health - NEUROFARBA - Pharmacology and Toxicology Section, University of Florence, Florence, Italy
| | - Alessandra Toti
- Department of Neuroscience, Psychology, Drug Research and Child Health - NEUROFARBA - Pharmacology and Toxicology Section, University of Florence, Florence, Italy
| | - Carla Ghelardini
- Department of Neuroscience, Psychology, Drug Research and Child Health - NEUROFARBA - Pharmacology and Toxicology Section, University of Florence, Florence, Italy
| | - Lorenzo Di Cesare Mannelli
- Department of Neuroscience, Psychology, Drug Research and Child Health - NEUROFARBA - Pharmacology and Toxicology Section, University of Florence, Florence, Italy.
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20
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Aslanzadeh M, Stanicek L, Tarbier M, Mármol-Sánchez E, Biryukova I, Friedländer M. Malat1 affects transcription and splicing through distinct pathways in mouse embryonic stem cells. NAR Genom Bioinform 2024; 6:lqae045. [PMID: 38711862 PMCID: PMC11071118 DOI: 10.1093/nargab/lqae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/14/2024] [Accepted: 04/30/2024] [Indexed: 05/08/2024] Open
Abstract
Malat1 is a long-noncoding RNA with critical roles in gene regulation and cancer metastasis, however its functional role in stem cells is largely unexplored. We here perform a nuclear knockdown of Malat1 in mouse embryonic stem cells, causing the de-regulation of 320 genes and aberrant splicing of 90 transcripts, some of which potentially affecting the translated protein sequence. We find evidence that Malat1 directly interacts with gene bodies and aberrantly spliced transcripts, and that it locates upstream of down-regulated genes at their putative enhancer regions, in agreement with functional genomics data. Consistent with this, we find these genes affected at both exon and intron levels, suggesting that they are transcriptionally regulated by Malat1. Besides, the down-regulated genes are regulated by specific transcription factors and bear both activating and repressive chromatin marks, suggesting that some of them might be regulated by bivalent promoters. We propose a model in which Malat1 facilitates the transcription of genes involved in chromatid dynamics and mitosis in one pathway, and affects the splicing of transcripts that are themselves involved in RNA processing in a distinct pathway. Lastly, we compare our findings with Malat1 perturbation studies performed in other cell systems and in vivo.
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Affiliation(s)
- Morteza Aslanzadeh
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Laura Stanicek
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Marcel Tarbier
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden
| | - Emilio Mármol-Sánchez
- Science for Life Laboratory and Center for Palaeogenetics. Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Inna Biryukova
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
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21
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Bahi A. Serotonin transporter knockdown relieves depression-like behavior and ethanol-induced CPP in mice after chronic social defeat stress. Behav Brain Res 2024; 466:114998. [PMID: 38614210 DOI: 10.1016/j.bbr.2024.114998] [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: 02/26/2024] [Revised: 04/09/2024] [Accepted: 04/09/2024] [Indexed: 04/15/2024]
Abstract
Patients with stress-triggered major depression disorders (MDD) can often seek comfort or temporary relief through alcohol consumption, as they may turn to it as a means of self-medication or coping with overwhelming emotions. The use of alcohol as a coping mechanism for stressful events can escalate, fostering a cycle where the temporary relief it provides from depression can deepen into alcohol dependence, exacerbating both conditions. Although, the specific mechanisms involved in stress-triggered alcohol dependence and MDD comorbidities are not well understood, a large body of literature suggests that the serotonin transporter (SERT) plays a critical role in these abnormalities. To further investigate this hypothesis, we used a lentiviral-mediated knockdown approach to examine the role of hippocampal SERT knockdown in social defeat stress-elicited depression like behavior and ethanol-induced place preference (CPP). The results showed that social defeat stress-pro depressant effects were reversed following SERT knockdown demonstrated by increased sucrose preference, shorter latency to feed in the novelty suppressed feeding test, and decreased immobility time in the tail suspension and forced swim tests. Moreover, and most importantly, social stress-induced ethanol-CPP acquisition and reinstatement were significantly reduced following hippocampal SERT knockdown using short hairpin RNA shRNA-expressing lentiviral vectors. Finally, we confirmed that SERT hippocampal mRNA expression correlated with measures of depression- and ethanol-related behaviors by Pearson's correlation analysis. Taken together, our data suggest that hippocampal serotoninergic system is involved in social stress-triggered mood disorders as well as in the acquisition and retrieval of ethanol contextual memory and that blockade of this transporter can decrease ethanol rewarding properties.
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Affiliation(s)
- Amine Bahi
- College of Medicine, Ajman University, Ajman, United Arab Emirates; Center of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates; Department of Anatomy, CMHS, UAE University, Al Ain, United Arab Emirates.
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22
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Koh H, Kang W, Mao YY, Park J, Kim S, Hong SH, Lee JH. Employment of diverse in vitro systems for analyzing multiple aspects of disease, hereditary hemorrhagic telangiectasia (HHT). Cell Biosci 2024; 14:65. [PMID: 38778363 PMCID: PMC11110195 DOI: 10.1186/s13578-024-01247-z] [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: 02/10/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND In vitro disease modeling enables translational research by providing insight into disease pathophysiology and molecular mechanisms, leading to the development of novel therapeutics. Nevertheless, in vitro systems have limitations for recapitulating the complexity of tissues, and a single model system is insufficient to gain a comprehensive understanding of a disease. RESULTS Here we explored the potential of using several models in combination to provide mechanistic insight into hereditary hemorrhagic telangiectasia (HHT), a genetic vascular disorder. Genome editing was performed to establish hPSCs (H9) with ENG haploinsufficiency and several in vitro models were used to recapitulate the functional aspects of the cells that constitute blood vessels. In a 2D culture system, endothelial cells showed early senescence, reduced viability, and heightened susceptibility to apoptotic insults, and smooth muscle cells (SMCs) exhibited similar behavior to their wild-type counterparts. Features of HHT were evident in 3D blood-vessel organoid systems, including thickening of capillary structures, decreased interaction between ECs and surrounding SMCs, and reduced cell viability. Features of ENG haploinsufficiency were observed in arterial and venous EC subtypes, with arterial ECs showing significant impairments. Molecular biological approaches confirmed the significant downregulation of Notch signaling in HHT-ECs. CONCLUSIONS Overall, we demonstrated refined research strategies to enhance our comprehension of HHT, providing valuable insights for pathogenic analysis and the exploration of innovative therapeutic interventions. Additionally, these results underscore the importance of employing diverse in vitro systems to assess multiple aspects of disease, which is challenging using a single in vitro system.
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Affiliation(s)
- Hyebin Koh
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Woojoo Kang
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, Republic of Korea
| | - Ying-Ying Mao
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea
- Department of Animal Science and Biotechnology, College of Agriculture and Life Science, Chungnam National University, Daejeon, Republic of Korea
| | - Jisoo Park
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Republic of Korea
| | - Sangjune Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Republic of Korea
| | - Seok-Ho Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, Republic of Korea.
- KW-Bio Co., Ltd, Chuncheon, South Korea.
| | - Jong-Hee Lee
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea.
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea.
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23
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Nakagawa S, Carnevali D, Tan X, Alvarez MJ, Parfitt DE, Di Vicino U, Arumugam K, Shin W, Aranda S, Normanno D, Sebastian-Perez R, Cannatá C, Cortes P, Neguembor MV, Shen MM, Califano A, Cosma MP. The Wnt-dependent master regulator NKX1-2 controls mouse pre-implantation development. Stem Cell Reports 2024; 19:689-709. [PMID: 38701778 PMCID: PMC11103935 DOI: 10.1016/j.stemcr.2024.04.004] [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: 06/23/2022] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 05/05/2024] Open
Abstract
Embryo size, specification, and homeostasis are regulated by a complex gene regulatory and signaling network. Here we used gene expression signatures of Wnt-activated mouse embryonic stem cell (mESC) clones to reverse engineer an mESC regulatory network. We identify NKX1-2 as a novel master regulator of preimplantation embryo development. We find that Nkx1-2 inhibition reduces nascent RNA synthesis, downregulates genes controlling ribosome biogenesis, RNA translation, and transport, and induces severe alteration of nucleolus structure, resulting in the exclusion of RNA polymerase I from nucleoli. In turn, NKX1-2 loss of function leads to chromosome missegregation in the 2- to 4-cell embryo stages, severe decrease in blastomere numbers, alterations of tight junctions (TJs), and impairment of microlumen coarsening. Overall, these changes impair the blastocoel expansion-collapse cycle and embryo cavitation, leading to altered lineage specification and developmental arrest.
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Affiliation(s)
- Shoma Nakagawa
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Davide Carnevali
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Xiangtian Tan
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Mariano J Alvarez
- Department of Systems Biology, Columbia University, New York, NY, USA; DarwinHealth Inc, New York, NY, USA
| | - David-Emlyn Parfitt
- Departments of Medicine, Genetics and Development, Urology, and Systems Biology, Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Umberto Di Vicino
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Karthik Arumugam
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - William Shin
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Sergi Aranda
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Davide Normanno
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Institute of Human Genetics, CNRS, Montpellier, France
| | - Ruben Sebastian-Perez
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Chiara Cannatá
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Paola Cortes
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Maria Victoria Neguembor
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Michael M Shen
- Department of Systems Biology, Columbia University, New York, NY, USA; Departments of Medicine, Genetics and Development, Urology, and Systems Biology, Herbert Irving Comprehensive Cancer Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA; Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA; Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA; Chan Zuckerberg Biohub New York, New York, NY, USA.
| | - Maria Pia Cosma
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; ICREA, Pg.Lluis Companys 23, 08010 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106 Zhongshan Er Road, Yuexiu District, Guangzhou 510080, China.
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Beckers P, Belo Do Nascimento I, Charlier M, Desmet N, Massie A, Hermans E. Implication of system x c- in neuroinflammation during the onset and maintenance of neuropathic pain. J Neuroinflammation 2024; 21:117. [PMID: 38715127 PMCID: PMC11077843 DOI: 10.1186/s12974-024-03112-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/25/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Despite the high prevalence of neuropathic pain, treating this neurological disease remains challenging, given the limited efficacy and numerous side effects associated with current therapies. The complexity in patient management is largely attributed to an incomplete understanding of the underlying pathological mechanisms. Central sensitization, that refers to the adaptation of the central nervous system to persistent inflammation and heightened excitatory transmission within pain pathways, stands as a significant contributor to persistent pain. Considering the role of the cystine/glutamate exchanger (also designated as system xc-) in modulating glutamate transmission and in supporting neuroinflammatory responses, we investigated the contribution of this exchanger in the development of neuropathic pain. METHODS We examined the implication of system xc- by evaluating changes in the expression/activity of this exchanger in the dorsal spinal cord of mice after unilateral partial sciatic nerve ligation. In this surgical model of neuropathic pain, we also examined the consequence of the genetic suppression of system xc- (using mice lacking the system xc- specific subunit xCT) or its pharmacological manipulation (using the pharmacological inhibitor sulfasalazine) on the pain-associated behavioral responses. Finally, we assessed the glial activation and the inflammatory response in the spinal cord by measuring mRNA and protein levels of GFAP and selected M1 and M2 microglial markers. RESULTS The sciatic nerve lesion was found to upregulate system xc- at the spinal level. The genetic deletion of xCT attenuated both the amplitude and the duration of the pain sensitization after nerve surgery, as evidenced by reduced responses to mechanical and thermal stimuli, and this was accompanied by reduced glial activation. Consistently, pharmacological inhibition of system xc- had an analgesic effect in lesioned mice. CONCLUSION Together, these observations provide evidence for a role of system xc- in the biochemical processes underlying central sensitization. We propose that the reduced hypersensitivity observed in the transgenic mice lacking xCT or in sulfasalazine-treated mice is mediated by a reduced gliosis in the lumbar spinal cord and/or a shift in microglial M1/M2 polarization towards an anti-inflammatory phenotype in the absence of system xc-. These findings suggest that drugs targeting system xc- could contribute to prevent or reduce neuropathic pain.
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Affiliation(s)
- Pauline Beckers
- Institute of Neuroscience, Group of Neuropharmacology, Université catholique de Louvain (UCLouvain), Avenue Hippocrate 53 (B1.53.01), Brussels, 1200, Belgium
| | - Inês Belo Do Nascimento
- Institute of Neuroscience, Group of Neuropharmacology, Université catholique de Louvain (UCLouvain), Avenue Hippocrate 53 (B1.53.01), Brussels, 1200, Belgium
| | - Mathilde Charlier
- Institute of Neuroscience, Group of Neuropharmacology, Université catholique de Louvain (UCLouvain), Avenue Hippocrate 53 (B1.53.01), Brussels, 1200, Belgium
| | - Nathalie Desmet
- Institute of Neuroscience, Group of Neuropharmacology, Université catholique de Louvain (UCLouvain), Avenue Hippocrate 53 (B1.53.01), Brussels, 1200, Belgium
| | - Ann Massie
- Neuro-Aging & Viro-Immunotherapy, Center for Neurosciences, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, Brussels, 1090, Belgium
| | - Emmanuel Hermans
- Institute of Neuroscience, Group of Neuropharmacology, Université catholique de Louvain (UCLouvain), Avenue Hippocrate 53 (B1.53.01), Brussels, 1200, Belgium.
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Hector M, Langmann T, Wolf A. Translocator protein (18 kDa) (Tspo) in the retina and implications for ocular diseases. Prog Retin Eye Res 2024; 100:101249. [PMID: 38430990 DOI: 10.1016/j.preteyeres.2024.101249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/05/2024]
Abstract
Translocator protein (18 kDa) (Tspo), formerly known as peripheral benzodiazepine receptor is a highly conserved transmembrane protein primarily located in the outer mitochondrial membrane. In the central nervous system (CNS), especially in glia cells, Tspo is upregulated upon inflammation. Consequently, Tspo was used as a tool for diagnostic in vivo imaging of neuroinflammation in the brain and as a potential therapeutic target. Several synthetic Tspo ligands have been explored as immunomodulatory and neuroprotective therapy approaches. Although the function of Tspo and how its ligands exert these beneficial effects is not fully clear, it became a research topic of interest, especially in ocular diseases in the past few years. This review summarizes state-of-the-art knowledge of Tspo expression and its proposed functions in different cells of the retina including microglia, retinal pigment epithelium and Müller cells. Tspo is involved in cytokine signaling, oxidative stress and reactive oxygen species production, calcium signaling, neurosteroid synthesis, energy metabolism, and cholesterol efflux. We also highlight recent developments in preclinical models targeting Tspo and summarize the relevance of Tspo biology for ocular and retinal diseases. We conclude that glial upregulation of Tspo in different ocular pathologies and the use of Tspo ligands as promising therapeutic approaches in preclinical studies underline the importance of Tspo as a potential disease-modifying protein.
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Affiliation(s)
- Mandy Hector
- Laboratory for Experimental Immunology of the Eye, Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
| | - Thomas Langmann
- Laboratory for Experimental Immunology of the Eye, Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
| | - Anne Wolf
- Laboratory for Experimental Immunology of the Eye, Department of Ophthalmology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
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26
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Lin JS, Petrera A, Hauck SM, Müller CL, Peters A, Thorand B. Associations of Proteomics With Hypertension and Systolic Blood Pressure: KORA S4/F4/FF4 and KORA Age1/Age2 Cohort Studies. Hypertension 2024; 81:1156-1166. [PMID: 38445514 PMCID: PMC11025610 DOI: 10.1161/hypertensionaha.123.22614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/19/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUND Hypertension, a complex condition, is primarily defined based on blood pressure readings without involving its pathophysiological mechanisms. We aimed to identify biomarkers through a proteomic approach, thereby enhancing the future definition of hypertension with insights into its molecular mechanisms. METHODS The discovery analysis included 1560 participants, aged 55 to 74 years at baseline, from the KORA (Cooperative Health Research in the Region of Augsburg) S4/F4/FF4 cohort study, with 3332 observations over a median of 13.4 years of follow-up. Generalized estimating equations were used to estimate the associations of 233 plasma proteins with hypertension and systolic blood pressure (SBP). For validation, proteins significantly associated with hypertension or SBP in the discovery analysis were validated in the KORA Age1/Age2 cohort study (1024 participants, 1810 observations). A 2-sample Mendelian randomization analysis was conducted to infer causalities of validated proteins with SBP. RESULTS Discovery analysis identified 49 proteins associated with hypertension and 99 associated with SBP. Validation in the KORA Age1/Age2 study replicated 7 proteins associated with hypertension and 23 associated with SBP. Three proteins, NT-proBNP (N-terminal pro-B-type natriuretic peptide), KIM1 (kidney injury molecule 1), and OPG (osteoprotegerin), consistently showed positive associations with both outcomes. Five proteins demonstrated potential causal associations with SBP in Mendelian randomization analysis, including NT-proBNP and OPG. CONCLUSIONS We identified and validated 7 hypertension-associated and 23 SBP-associated proteins across 2 cohort studies. KIM1, NT-proBNP, and OPG demonstrated robust associations, and OPG was identified for the first time as associated with blood pressure. For NT-proBNP (protective) and OPG, causal associations with SBP were suggested.
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Affiliation(s)
- Jie-sheng Lin
- Institute of Epidemiology (J.-s.L., A. Peters, B.T.), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Faculty of Medicine, LMU Munich, Pettenkofer School of Public Health, Munich, Germany (J.-s.L., B.T.)
| | - Agnese Petrera
- Metabolomics and Proteomics Core (A. Petrera, S.M.H.), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Stefanie M. Hauck
- Metabolomics and Proteomics Core (A. Petrera, S.M.H.), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Christian L. Müller
- Institute of Computational Biology (C.L.M.), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Department of Statistics (C.L.M.), Ludwig-Maximilians-Universität München, Munich, Germany
- Center for Computational Mathematics, Flatiron Institute, New York, NY (C.L.M.)
| | - Annette Peters
- Institute of Epidemiology (J.-s.L., A. Peters, B.T.), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Chair of Epidemiology, Institute for Medical Information Processing, Biometry and Epidemiology, Medical Faculty (A. Peters), Ludwig-Maximilians-Universität München, Munich, Germany
- German Center for Diabetes Research, Partner München-Neuherberg, Germany (A. Peters, B.T.)
| | - Barbara Thorand
- Institute of Epidemiology (J.-s.L., A. Peters, B.T.), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Faculty of Medicine, LMU Munich, Pettenkofer School of Public Health, Munich, Germany (J.-s.L., B.T.)
- German Center for Diabetes Research, Partner München-Neuherberg, Germany (A. Peters, B.T.)
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Shahi S, Kang T, Fonseka P. Extracellular Vesicles in Pathophysiology: A Prudent Target That Requires Careful Consideration. Cells 2024; 13:754. [PMID: 38727289 PMCID: PMC11083420 DOI: 10.3390/cells13090754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Extracellular vesicles (EVs) are membrane-bound particles released by cells to perform multitudes of biological functions. Owing to their significant implications in diseases, the pathophysiological role of EVs continues to be extensively studied, leading research to neglect the need to explore their role in normal physiology. Despite this, many identified physiological functions of EVs, including, but not limited to, tissue repair, early development and aging, are attributed to their modulatory role in various signaling pathways via intercellular communication. EVs are widely perceived as a potential therapeutic strategy for better prognosis, primarily through utilization as a mode of delivery vehicle. Moreover, disease-associated EVs serve as candidates for the targeted inhibition by pharmacological or genetic means. However, these attempts are often accompanied by major challenges, such as off-target effects, which may result in adverse phenotypes. This renders the clinical efficacy of EVs elusive, indicating that further understanding of the specific role of EVs in physiology may enhance their utility. This review highlights the essential role of EVs in maintaining cellular homeostasis under different physiological settings, and also discusses the various aspects that may potentially hinder the robust utility of EV-based therapeutics.
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Affiliation(s)
| | | | - Pamali Fonseka
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia; (S.S.); (T.K.)
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28
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Karas BF, Terez KR, Mowla S, Battula N, Flannery KP, Gural BM, Aboussleman G, Mubin N, Manzini MC. Removal of pomt1 in zebrafish leads to loss of α-dystroglycan glycosylation and dystroglycanopathy phenotypes. Hum Mol Genet 2024; 33:709-723. [PMID: 38272461 PMCID: PMC11000664 DOI: 10.1093/hmg/ddae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 11/28/2023] [Accepted: 12/22/2023] [Indexed: 01/27/2024] Open
Abstract
Biallelic mutations in Protein O-mannosyltransferase 1 (POMT1) are among the most common causes of a severe group of congenital muscular dystrophies (CMDs) known as dystroglycanopathies. POMT1 is a glycosyltransferase responsible for the attachment of a functional glycan mediating interactions between the transmembrane glycoprotein dystroglycan and its binding partners in the extracellular matrix (ECM). Disruptions in these cell-ECM interactions lead to multiple developmental defects causing brain and eye malformations in addition to CMD. Removing Pomt1 in the mouse leads to early embryonic death due to the essential role of dystroglycan during placental formation in rodents. Here, we characterized and validated a model of pomt1 loss of function in the zebrafish showing that developmental defects found in individuals affected by dystroglycanopathies can be recapitulated in the fish. We also discovered that pomt1 mRNA provided by the mother in the oocyte supports dystroglycan glycosylation during the first few weeks of development. Muscle disease, retinal synapse formation deficits, and axon guidance defects can only be uncovered during the first week post fertilization by generating knock-out embryos from knock-out mothers. Conversely, maternal pomt1 from heterozygous mothers was sufficient to sustain muscle, eye, and brain development only leading to loss of photoreceptor synapses at 30 days post fertilization. Our findings show that it is important to define the contribution of maternal mRNA while developing zebrafish models of dystroglycanopathies and that offspring generated from heterozygous and knock-out mothers can be used to differentiate the role of dystroglycan glycosylation in tissue formation and maintenance.
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Affiliation(s)
- Brittany F Karas
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers University-Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Kristin R Terez
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers University-Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Shorbon Mowla
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers University-Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Namarata Battula
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers University-Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Kyle P Flannery
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers University-Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Brian M Gural
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers University-Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Grace Aboussleman
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers University-Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - Numa Mubin
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers University-Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
| | - M Chiara Manzini
- Department of Neuroscience and Cell Biology, Child Health Institute of New Jersey, Rutgers University-Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States
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Trampert DC, Kersten R, Tolenaars D, Jongejan A, van de Graaf SF, Beuers U. Laminin 511-E8, an autoantigen in IgG4-related cholangitis, contributes to cholangiocyte protection. JHEP Rep 2024; 6:101015. [PMID: 38524667 PMCID: PMC10959701 DOI: 10.1016/j.jhepr.2024.101015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 01/04/2024] [Accepted: 01/11/2024] [Indexed: 03/26/2024] Open
Abstract
Background & Aims IgG4-related cholangitis (IRC) is the hepatobiliary manifestation of IgG4-related disease. Anti-laminin 511-E8 autoantibodies have been identified in its pancreatic manifestation. Laminin 511-E8 promotes endothelial barrier function, lymphocyte recruitment, and cholangiocyte differentiation. Here, we investigate anti-laminin 511-E8 autoantibody presence in IRC, and mechanisms via which laminin 511 may contribute to cholangiocyte protection. Methods Anti-laminin 511-E8 serum autoantibody positivity was assessed by ELISA. RNA sequencing and RT-qPCR were performed on human H69 cholangiocytes treated with recombinant laminin 511-E8. H69 cholangiocytes were subjected to shRNA knockdown targeting genes encoding laminin 511 (LAMA5, LAMB1, LAMC1) or treated with recombinant laminin 511-E8. Cholangiocellular bile acid influx was quantified radiochemically using 22,23-3H-glycochenodeoxycholic acid (GCDC). GCDC-induced apoptosis was determined by Caspase-3/7 assays. Cholangiocellular barrier function was assessed by FITC-Dextran permeability assays. Immunofluorescent staining of laminin 511 and claudin 1 was performed on extrahepatic bile duct tissue of control and anti-laminin 511-E8 positive individuals with IRC. Results Seven out of 52 individuals with IRC had autoantibodies against laminin 511-E8. Recombinant laminin 511-E8 led to differential expression of genes involved in secretion, barrier function, and inflammation. Knockdown of laminin 511 constituents increased toxic bile acid permeation and GCDC-induced apoptosis. Laminin 511-E8 treatment decreased toxic bile acid permeation and dose-dependently alleviated GCDC-induced apoptosis. LAMA5 and LAMC1 knockdown increased transepithelial permeability. Laminin 511-E8 treatment reduced transepithelial permeability and prevented T lymphocyte-induced barrier dysfunction. Laminin 511 and claudin 1 staining patterns appeared altered in anti-laminin 511-E8 positive individuals with IRC. Conclusions Laminin 511-E8 is an autoantigen in subsets of individuals with IRC. Laminin 511 enhances cholangiocellular barrier function and protects cholangiocytes against T lymphocyte-induced barrier dysfunction, toxic bile acid permeation and bile acid-induced apoptosis. Impact and implications A subset of patients with IgG4-related cholangitis (IRC) has autoantibodies against laminin 511-E8. In human cholangiocytes, laminin 511 protects against (T lymphocyte-induced) epithelial barrier dysfunction and hydrophobic bile acids. Laminin 511 and claudin 1 staining may be altered in extrahepatic bile ducts of patients with IRC who are anti-laminin 511-E8 positive. This makes it tempting to speculate that a decreased epithelial barrier function with attraction of immune cells and impaired bicarbonate secretion as a result of dysfunction of laminin 511 by autoantibody binding could potentially be a common systemic pathogenic mechanism in a subset of patients with IgG4-RD.
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Affiliation(s)
- David C. Trampert
- Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Remco Kersten
- Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Dagmar Tolenaars
- Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Aldo Jongejan
- Department of Epidemiology & Data Science, Bioinformatics Laboratory, Amsterdam Public Health Research Institute, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Stan F.J. van de Graaf
- Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ulrich Beuers
- Department of Gastroenterology and Hepatology, Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
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30
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Lu D, Zhi Y, Su H, Lin X, Lin J, Shi Y, Yi W, Hong C, Zhang T, Fu Z, Chen LY, Zhao Z, Li R, Xu Z, Chen W, Wang N, Xu D. ESCRT-I protein UBAP1 controls ventricular expansion and cortical neurogenesis via modulating adherens junctions of radial glial cells. Cell Rep 2024; 43:113818. [PMID: 38402586 DOI: 10.1016/j.celrep.2024.113818] [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: 08/17/2023] [Revised: 12/26/2023] [Accepted: 02/01/2024] [Indexed: 02/27/2024] Open
Abstract
Intricate cerebral cortex formation is orchestrated by the precise behavior and division dynamics of radial glial cells (RGCs). Endocytosis functions in the recycling and remodeling of adherens junctions (AJs) in response to changes in RGC activity and function. Here, we show that conditional disruption of ubiquitin-associated protein 1 (UBAP1), a component of endosomal sorting complex required for transport (ESCRT), causes severe brain dysplasia and prenatal ventriculomegaly. UBAP1 depletion disrupts the AJs and polarity of RGCs, leading to failure of apically directed interkinetic nuclear migration. Accordingly, UBAP1 knockout or knockdown results in reduced proliferation and precocious differentiation of neural progenitor cells. Mechanistically, UBAP1 regulates the expression and surface localization of cell adhesion molecules, and β-catenin over-expression significantly rescues the phenotypes of Ubap1 knockdown in vivo. Our study reveals a critical physiological role of the ESCRT machinery in cortical neurogenesis by regulating AJs of RGCs.
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Affiliation(s)
- Danping Lu
- Fujian Key Laboratory of Molecular Neurology, Institute of Neuroscience, Fujian Medical University, Fuzhou 350004, China; College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yiqiang Zhi
- Fujian Key Laboratory of Molecular Neurology, Institute of Neuroscience, Fujian Medical University, Fuzhou 350004, China; School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China
| | - Huizhen Su
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Xiang Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Jingjing Lin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Yan Shi
- Fujian Key Laboratory of Molecular Neurology, Institute of Neuroscience, Fujian Medical University, Fuzhou 350004, China
| | - Wenxiang Yi
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China
| | - Chaoyin Hong
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China
| | - Tongtong Zhang
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China
| | - Zhifei Fu
- Public Technology Service Center, Fujian Medical University, Fuzhou 350122, China
| | - Li-Yu Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhiqi Zhao
- State Key Laboratory of Molecular Developmental Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Rong Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Zhiheng Xu
- State Key Laboratory of Molecular Developmental Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wanjin Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China.
| | - Ning Wang
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou 350005, China.
| | - Dan Xu
- Fujian Key Laboratory of Molecular Neurology, Institute of Neuroscience, Fujian Medical University, Fuzhou 350004, China.
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Shi H, Williams MJ, Satas G, Weiner AC, McPherson A, Shah SP. Allele-specific transcriptional effects of subclonal copy number alterations enable genotype-phenotype mapping in cancer cells. Nat Commun 2024; 15:2482. [PMID: 38509111 PMCID: PMC10954741 DOI: 10.1038/s41467-024-46710-0] [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: 01/18/2023] [Accepted: 03/01/2024] [Indexed: 03/22/2024] Open
Abstract
Subclonal copy number alterations are a prevalent feature in tumors with high chromosomal instability and result in heterogeneous cancer cell populations with distinct phenotypes. However, the extent to which subclonal copy number alterations contribute to clone-specific phenotypes remains poorly understood. We develop TreeAlign, which computationally integrates independently sampled single-cell DNA and RNA sequencing data from the same cell population. TreeAlign accurately encodes dosage effects from subclonal copy number alterations, the impact of allelic imbalance on allele-specific transcription, and obviates the need to define genotypic clones from a phylogeny a priori, leading to highly granular definitions of clones with distinct expression programs. These improvements enable clone-clone gene expression comparisons with higher resolution and identification of expression programs that are genomically independent. Our approach sets the stage for dissecting the relative contribution of fixed genomic alterations and dynamic epigenetic processes on gene expression programs in cancer.
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Affiliation(s)
- Hongyu Shi
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY, USA
| | - Marc J Williams
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gryte Satas
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Adam C Weiner
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andrew McPherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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32
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Wang X, Li A, Li X, Cui H. Empowering Protein Engineering through Recombination of Beneficial Substitutions. Chemistry 2024; 30:e202303889. [PMID: 38288640 DOI: 10.1002/chem.202303889] [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: 01/04/2024] [Indexed: 02/24/2024]
Abstract
Directed evolution stands as a seminal technology for generating novel protein functionalities, a cornerstone in biocatalysis, metabolic engineering, and synthetic biology. Today, with the development of various mutagenesis methods and advanced analytical machines, the challenge of diversity generation and high-throughput screening platforms is largely solved, and one of the remaining challenges is: how to empower the potential of single beneficial substitutions with recombination to achieve the epistatic effect. This review overviews experimental and computer-assisted recombination methods in protein engineering campaigns. In addition, integrated and machine learning-guided strategies were highlighted to discuss how these recombination approaches contribute to generating the screening library with better diversity, coverage, and size. A decision tree was finally summarized to guide the further selection of proper recombination strategies in practice, which was beneficial for accelerating protein engineering.
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Affiliation(s)
- Xinyue Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Anni Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Haiyang Cui
- School of Life Sciences, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
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Jain N, Shashi Bhushan BL, Natarajan M, Mehta R, Saini DK, Chatterjee K. Advanced 3D In Vitro Lung Fibrosis Models: Contemporary Status, Clinical Uptake, and Prospective Outlooks. ACS Biomater Sci Eng 2024; 10:1235-1261. [PMID: 38335198 DOI: 10.1021/acsbiomaterials.3c01499] [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: 02/12/2024]
Abstract
Fibrosis has been characterized as a global health problem and ranks as one of the primary causes of organ dysfunction. Currently, there is no cure for pulmonary fibrosis, and limited therapeutic options are available due to an inadequate understanding of the disease pathogenesis. The absence of advanced in vitro models replicating dynamic temporal changes observed in the tissue with the progression of the disease is a significant impediment in the development of novel antifibrotic treatments, which has motivated research on tissue-mimetic three-dimensional (3D) models. In this review, we summarize emerging trends in preparing advanced lung models to recapitulate biochemical and biomechanical processes associated with lung fibrogenesis. We begin by describing the importance of in vivo studies and highlighting the often poor correlation between preclinical research and clinical outcomes and the limitations of conventional cell culture in accurately simulating the 3D tissue microenvironment. Rapid advancement in biomaterials, biofabrication, biomicrofluidics, and related bioengineering techniques are enabling the preparation of in vitro models to reproduce the epithelium structure and operate as reliable drug screening strategies for precise prediction. Improving and understanding these model systems is necessary to find the cross-talks between growing cells and the stage at which myofibroblasts differentiate. These advanced models allow us to utilize the knowledge and identify, characterize, and hand pick medicines beneficial to the human community. The challenges of the current approaches, along with the opportunities for further research with potential for translation in this field, are presented toward developing novel treatments for pulmonary fibrosis.
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Affiliation(s)
- Nipun Jain
- Department of Materials Engineering, Indian Institute of Science, C.V Raman Avenue, Bangalore 560012 India
| | - B L Shashi Bhushan
- Department of Pulmonary Medicine, Victoria Hospital, Bangalore Medical College and Research Institute, Bangalore 560002 India
| | - M Natarajan
- Department of Pathology, Victoria Hospital, Bangalore Medical College and Research Institute, Bangalore 560002 India
| | - Ravi Mehta
- Department of Pulmonology and Critical Care, Apollo Hospitals, Jayanagar, Bangalore 560011 India
| | - Deepak Kumar Saini
- Department of Developmental Biology and Genetics, Indian Institute of Science, C.V Raman Avenue, Bangalore 560012 India
| | - Kaushik Chatterjee
- Department of Materials Engineering, Indian Institute of Science, C.V Raman Avenue, Bangalore 560012 India
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Anversa RG, Maddern XJ, Lawrence AJ, Walker LC. Orphan peptide and G protein-coupled receptor signalling in alcohol use disorder. Br J Pharmacol 2024; 181:595-609. [PMID: 38073127 PMCID: PMC10953447 DOI: 10.1111/bph.16301] [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: 10/14/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 01/10/2024] Open
Abstract
Neuropeptides and G protein-coupled receptors (GPCRs) have long been, and continue to be, one of the most popular target classes for drug discovery in CNS disorders, including alcohol use disorder (AUD). Yet, orphaned neuropeptide systems and receptors (oGPCR), which have no known cognate receptor or ligand, remain understudied in drug discovery and development. Orphan neuropeptides and oGPCRs are abundantly expressed within the brain and represent an unprecedented opportunity to address brain function and may hold potential as novel treatments for disease. Here, we describe the current literature regarding orphaned neuropeptides and oGPCRs implicated in AUD. Specifically, in this review, we focus on the orphaned neuropeptide cocaine- and amphetamine-regulated transcript (CART), and several oGPCRs that have been directly implicated in AUD (GPR6, GPR26, GPR88, GPR139, GPR158) and discuss their potential and pitfalls as novel treatments, and progress in identifying their cognate receptors or ligands.
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Affiliation(s)
- Roberta Goncalves Anversa
- Florey Institute of Neuroscience and Mental HealthMelbourneVICAustralia
- Florey Department of Neuroscience and Mental HealthUniversity of MelbourneMelbourneVICAustralia
| | - Xavier J. Maddern
- Florey Institute of Neuroscience and Mental HealthMelbourneVICAustralia
- Florey Department of Neuroscience and Mental HealthUniversity of MelbourneMelbourneVICAustralia
| | - Andrew J. Lawrence
- Florey Institute of Neuroscience and Mental HealthMelbourneVICAustralia
- Florey Department of Neuroscience and Mental HealthUniversity of MelbourneMelbourneVICAustralia
| | - Leigh C. Walker
- Florey Institute of Neuroscience and Mental HealthMelbourneVICAustralia
- Florey Department of Neuroscience and Mental HealthUniversity of MelbourneMelbourneVICAustralia
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Koo J, Zhu GH, Palli SR. CRISPR-Cas9 mediated dsRNase knockout improves RNAi efficiency in the fall armyworm. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 200:105839. [PMID: 38582601 DOI: 10.1016/j.pestbp.2024.105839] [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: 12/27/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 04/08/2024]
Abstract
Lepidopteran insects are refractory to RNA interference (RNAi) response, especially to orally delivered double-stranded RNA (dsRNA). High nuclease activity in the midgut lumen is proposed as one of the major reasons for RNAi insensitivity. We identified three dsRNase genes highly expressed in the midgut of fall armyworm (FAW), Spodoptera frugiperda. The genomic region harboring those three dsRNase genes was deleted using the CRISPR-Cas9-mediated genome editing method. A homozygous line with deletion of three dsRNase genes was produced. dsRNA degradation by midgut lumen contents of mutant larvae was lower than in wild-type larvae. Feeding dsRNA targeting the inhibitor of apoptosis (IAP) gene increased knockdown of the target gene and mortality in mutants compared to wild-type larvae. These results suggest that dsRNases in the midgut contribute to RNAi inefficiency in FAW. Formulations that protect dsRNA from dsRNase degradation may improve RNAi efficiency in FAW and other lepidopteran insects.
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Affiliation(s)
- Jinmo Koo
- Department of Entomology, College of Agriculture, University of Kentucky, Lexington, KY 40546, USA
| | - Guan-Heng Zhu
- Department of Entomology, College of Agriculture, University of Kentucky, Lexington, KY 40546, USA
| | - Subba Reddy Palli
- Department of Entomology, College of Agriculture, University of Kentucky, Lexington, KY 40546, USA.
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Mitrovic K, Zivotic I, Kolic I, Zakula J, Zivkovic M, Stankovic A, Jovanovic I. A preliminary study of the miRNA restitution effect on CNV-induced miRNA downregulation in CAKUT. BMC Genomics 2024; 25:218. [PMID: 38413914 PMCID: PMC10900603 DOI: 10.1186/s12864-024-10121-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 02/14/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND The majority of CAKUT-associated CNVs overlap at least one miRNA gene, thus affecting the cellular levels of the corresponding miRNA. We aimed to investigate the potency of restitution of CNV-affected miRNA levels to remediate the dysregulated expression of target genes involved in kidney physiology and development in vitro. METHODS Heterozygous MIR484 knockout HEK293 and homozygous MIR185 knockout HEK293 cell lines were used as models depicting the deletion of the frequently affected miRNA genes by CAKUT-associated CNVs. After treatment with the corresponding miRNA mimics, the levels of the target genes have been compared to the non-targeting control treatment. For both investigated miRNAs, MDM2 and PKD1 were evaluated as common targets, while additional 3 genes were investigated as targets of each individual miRNA (NOTCH3, FIS1 and APAF1 as hsa-miR-484 targets and RHOA, ATF6 and CDC42 as hsa-miR-185-5p targets). RESULTS Restitution of the corresponding miRNA levels in both knockout cell lines has induced a change in the mRNA levels of certain candidate target genes, thus confirming the potential to alleviate the CNV effect on miRNA expression. Intriguingly, HEK293 WT treatment with investigated miRNA mimics has triggered a more pronounced effect, thus suggesting the importance of miRNA interplay in different genomic contexts. CONCLUSIONS Dysregulation of multiple mRNA targets mediated by CNV-affected miRNAs could represent the underlying mechanism behind the unresolved CAKUT occurrence and phenotypic variability observed in CAKUT patients. Characterizing miRNAs located in CNVs and their potential to become molecular targets could eventually help in understanding and improving the management of CAKUT.
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Affiliation(s)
- Kristina Mitrovic
- Department of Radiobiology and Molecular Genetics, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11001, Belgrade, P.O. Box 522, Serbia
| | - Ivan Zivotic
- Department of Radiobiology and Molecular Genetics, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11001, Belgrade, P.O. Box 522, Serbia
| | - Ivana Kolic
- Department of Radiobiology and Molecular Genetics, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11001, Belgrade, P.O. Box 522, Serbia
| | - Jelena Zakula
- Department of Molecular Biology and Endocrinology, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11001, Belgrade, P.O. Box 522, Serbia
| | - Maja Zivkovic
- Department of Radiobiology and Molecular Genetics, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11001, Belgrade, P.O. Box 522, Serbia
| | - Aleksandra Stankovic
- Department of Radiobiology and Molecular Genetics, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11001, Belgrade, P.O. Box 522, Serbia
| | - Ivan Jovanovic
- Department of Radiobiology and Molecular Genetics, "Vinča" Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, 11001, Belgrade, P.O. Box 522, Serbia.
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Yang M, Diaz F, Krause ART, Lei Y, Liu WS. Synergistic enhancement of the mouse Pramex1 and Pramel1 in repressing retinoic acid (RA) signaling during gametogenesis. Cell Biosci 2024; 14:28. [PMID: 38395975 PMCID: PMC10893636 DOI: 10.1186/s13578-024-01212-w] [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: 12/07/2023] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND PRAME constitutes one of the largest multi-copy gene families in Eutherians, encoding cancer-testis antigens (CTAs) with leucine-rich repeats (LRR) domains, highly expressed in cancer cells and gametogenic germ cells. This study aims to elucidate genetic interactions between two members, Pramex1 and Pramel1, in the mouse Prame family during gametogenesis using a gene knockout approach. RESULT Single-gene knockout (sKO) of either Pramex1 or Pramel1 resulted in approximately 7% of abnormal seminiferous tubules, characterized by a Sertoli-cell only (SCO) phenotype, impacting sperm count and fecundity significantly. Remarkably, sKO female mice displayed normal reproductive functions. In contrast, Pramex1/Pramel1 double knockout (dKO) mice exhibited reduced fecundity in both sexes. In dKO females, ovarian primary follicle count decreased by 50% compared to sKO and WT mice, correlating with a 50% fecundity decrease. This suggested compensatory roles during oogenesis in Pramex1 or Pramel1 sKO females. Conversely, dKO males showed an 18% frequency of SCO tubules, increased apoptotic germ cells, and decreased undifferentiated spermatogonia compared to sKO and WT testes. Western blot analysis with PRAMEX1- or PRAMEL1-specific antibodies on sKO testes revealed compensatory upregulation of each protein (30-50%) in response to the other gene's deletion. Double KO males exhibited more severe defects in sperm count and litter size, surpassing Pramex1 and Pramel1 sKO accumulative effects, indicating a synergistic enhancement interaction during spermatogenesis. Additional experiments administering trans-retinoic acid (RA) and its inhibitor (WIN18,446) in sKO, dKO, and WT mice suggested that PRAMEX1 and PRAMEL1 synergistically repress the RA signaling pathway during spermatogenesis. CONCLUSION Data from sKO and dKO mice unveil a synergistic interaction via the RA signaling pathway between Pramex1 and Pramel1 genes during gametogenesis. This discovery sets the stage for investigating interactions among other members within the Prame family, advancing our understanding of multi-copy gene families involved in germ cell formation and function.
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Affiliation(s)
- Mingyao Yang
- Department of Animal Science, Center for Reproductive Biology and Health (CRBH), College of Agricultural Sciences, The Pennsylvania State University, 311 AVBS Building, University Park, PA, 16802, USA
| | - Francisco Diaz
- Department of Animal Science, Center for Reproductive Biology and Health (CRBH), College of Agricultural Sciences, The Pennsylvania State University, 311 AVBS Building, University Park, PA, 16802, USA
| | - Ana Rita T Krause
- Department of Animal Science, Center for Reproductive Biology and Health (CRBH), College of Agricultural Sciences, The Pennsylvania State University, 311 AVBS Building, University Park, PA, 16802, USA
| | - Yuguo Lei
- Department of Biomedical Engineering, College of Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Wan-Sheng Liu
- Department of Animal Science, Center for Reproductive Biology and Health (CRBH), College of Agricultural Sciences, The Pennsylvania State University, 311 AVBS Building, University Park, PA, 16802, USA.
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38
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Rayi S, Cai Y, Greenwich JL, Fuqua C, Gerdt JP. Interbacterial Biofilm Competition through a Suite of Secreted Metabolites. ACS Chem Biol 2024; 19:462-470. [PMID: 38261537 PMCID: PMC10951839 DOI: 10.1021/acschembio.3c00655] [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: 01/25/2024]
Abstract
Polymicrobial biofilms are ubiquitous, and the complex interspecies interactions within them are cryptic. We discovered the chemical foundation of antagonistic interactions in a model dual-species biofilm in which Pseudomonas aeruginosa inhibits the biofilm formation of Agrobacterium tumefaciens. Three known siderophores produced by P. aeruginosa (pyoverdine, pyochelin, and dihydroaeruginoic acid) were each capable of inhibiting biofilm formation. Surprisingly, a mutant that was incapable of producing these siderophores still secreted an antibiofilm metabolite. We discovered that this inhibitor was N5-formyl-N5-hydroxy-l-ornithine (fOHOrn)─a precursor in pyoverdine biosynthesis. Unlike the siderophores, this inhibitor did not appear to function via extracellular metal sequestration. In addition to this discovery, the compensatory overproduction of a new biofilm inhibitor illustrates the risk of pleiotropy in genetic knockout experiments. In total, this work lends new insight into the chemical nature of dual-species biofilm regulation and reveals a new naturally produced inhibitor of A. tumefaciens biofilm formation.
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Affiliation(s)
- Soniya Rayi
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Yanyao Cai
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jennifer L Greenwich
- Department of Biology, Indiana University, Bloomington, Indiana 47405, United States
| | - Clay Fuqua
- Department of Biology, Indiana University, Bloomington, Indiana 47405, United States
| | - Joseph P Gerdt
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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Zheng Y, Chen S. Transcriptional precision in photoreceptor development and diseases - Lessons from 25 years of CRX research. Front Cell Neurosci 2024; 18:1347436. [PMID: 38414750 PMCID: PMC10896975 DOI: 10.3389/fncel.2024.1347436] [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: 11/30/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024] Open
Abstract
The vertebrate retina is made up of six specialized neuronal cell types and one glia that are generated from a common retinal progenitor. The development of these distinct cell types is programmed by transcription factors that regulate the expression of specific genes essential for cell fate specification and differentiation. Because of the complex nature of transcriptional regulation, understanding transcription factor functions in development and disease is challenging. Research on the Cone-rod homeobox transcription factor CRX provides an excellent model to address these challenges. In this review, we reflect on 25 years of mammalian CRX research and discuss recent progress in elucidating the distinct pathogenic mechanisms of four CRX coding variant classes. We highlight how in vitro biochemical studies of CRX protein functions facilitate understanding CRX regulatory principles in animal models. We conclude with a brief discussion of the emerging systems biology approaches that could accelerate precision medicine for CRX-linked diseases and beyond.
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Affiliation(s)
- Yiqiao Zheng
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
| | - Shiming Chen
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
- Department of Developmental Biology, Washington University in St. Louis, Saint Louis, MO, United States
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Pyrillou K, Humphry M, Kitt LA, Rodgers A, Nus M, Bennett MR, Smith KG, Lyons PA, Mallat Z, Clarke MC. Loss of T follicular regulatory cell-derived IL-1R2 augments germinal center reactions via increased IL-1. JCI Insight 2024; 9:e174005. [PMID: 38329807 PMCID: PMC11143922 DOI: 10.1172/jci.insight.174005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 01/31/2024] [Indexed: 02/10/2024] Open
Abstract
Inappropriate immune activity is key in the pathogenesis of multiple diseases, and it is typically driven by excess inflammation and/or autoimmunity. IL-1 is often the effector owing to its powerful role in both innate and adaptive immunity, and, thus, it is tightly controlled at multiple levels. IL-1R2 antagonizes IL-1, but effects of losing this regulation are unknown. We found that IL-1R2 resolves inflammation by rapidly scavenging free IL-1. Specific IL-1R2 loss in germinal center (GC) T follicular regulatory (Tfr) cells increased the GC response after a first, but not booster, immunization, with an increase in T follicular helper (Tfh) cells, GC B cells, and antigen-specific antibodies, which was reversed upon IL-1 blockade. However, IL-1 signaling is not obligate for GC reactions, as WT and Il1r1-/- mice showed equivalent phenotypes, suggesting that GC IL-1 is normally restrained by IL-1R2. Fascinatingly, germline Il1r2-/- mice did not show this phenotype, but conditional Il1r2 deletion in adulthood recapitulated it, implying that compensation during development counteracts IL-1R2 loss. Finally, patients with ulcerative colitis or Crohn's disease had lower serum IL-1R2. All together, we show that IL-1R2 controls important aspects of innate and adaptive immunity and that IL-1R2 level may contribute to human disease propensity and/or progression.
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Affiliation(s)
- Katerina Pyrillou
- Section of CardioRespiratory Medicine, Heart and Lung Research Institute, and
| | - Melanie Humphry
- Section of CardioRespiratory Medicine, Heart and Lung Research Institute, and
| | - Lauren A. Kitt
- Section of CardioRespiratory Medicine, Heart and Lung Research Institute, and
| | - Amanda Rodgers
- Section of CardioRespiratory Medicine, Heart and Lung Research Institute, and
| | - Meritxell Nus
- Section of CardioRespiratory Medicine, Heart and Lung Research Institute, and
| | - Martin R. Bennett
- Section of CardioRespiratory Medicine, Heart and Lung Research Institute, and
| | - Kenneth G.C. Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Paul A. Lyons
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Ziad Mallat
- Section of CardioRespiratory Medicine, Heart and Lung Research Institute, and
| | - Murray C.H. Clarke
- Section of CardioRespiratory Medicine, Heart and Lung Research Institute, and
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LaCoursiere CM, Ullmann JFP, Koh HY, Turner L, Baker CM, Robens B, Shao W, Rotenberg A, McGraw CM, Poduri A. Zebrafish models of candidate human epilepsy-associated genes provide evidence of hyperexcitability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.07.579190. [PMID: 38370728 PMCID: PMC10871320 DOI: 10.1101/2024.02.07.579190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Hundreds of novel candidate human epilepsy-associated genes have been identified thanks to advancements in next-generation sequencing and large genome-wide association studies, but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy-associated genes, of which 81 were determined suitable for the generation of loss-of-function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants, 48 were successfully established as stable mutant lines and assessed for seizure-like swim patterns in a primary F2 screen. Evidence of seizure-like behavior was present in 5 (arfgef1, kcnd2, kcnv1, ubr5, wnt8b) of the 48 mutant lines assessed. Further characterization of those 5 lines provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally, arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Furthermore, RNAseq revealed convergent transcriptional abnormalities between mutant lines, consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1, KCND2, and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.
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Affiliation(s)
- Christopher Mark LaCoursiere
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Jeremy F P Ullmann
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Hyun Yong Koh
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Departments of Neuroscience and Pediatrics, Division of Neurology and Developmental Neuroscience, BCM, Houston, Texas, USA
| | - Laura Turner
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Cristina M Baker
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| | - Barbara Robens
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Wanqing Shao
- Research Computing, Department of Information Technology, Boston Children's Hospital, Boston, MA, USA
| | - Alexander Rotenberg
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher M McGraw
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Annapurna Poduri
- F.M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
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Zhao S, Zhao H, Zhao L, Cheng X, Zheng Z, Wu M, Wen W, Wang S, Zhou Z, Xie H, Ruan D, Li Q, Liu X, Ou C, Li G, Zhao Z, Chen G, Niu Y, Yin X, Hu Y, Zhang X, Liu P, Qiu G, Liu W, Zhao C, Wu Z, Zhang J, Wu N. Unraveling the genetic architecture of congenital vertebral malformation with reference to the developing spine. Nat Commun 2024; 15:1125. [PMID: 38321032 PMCID: PMC10847475 DOI: 10.1038/s41467-024-45442-5] [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: 09/02/2023] [Accepted: 01/23/2024] [Indexed: 02/08/2024] Open
Abstract
Congenital vertebral malformation, affecting 0.13-0.50 per 1000 live births, has an immense locus heterogeneity and complex genetic architecture. In this study, we analyze exome/genome sequencing data from 873 probands with congenital vertebral malformation and 3794 control individuals. Clinical interpretation identifies Mendelian etiologies in 12.0% of the probands and reveals a muscle-related disease mechanism. Gene-based burden test of ultra-rare variants identifies risk genes with large effect sizes (ITPR2, TBX6, TPO, H6PD, and SEC24B). To further investigate the biological relevance of the genetic association signals, we perform single-nucleus RNAseq on human embryonic spines. The burden test signals are enriched in the notochord at early developmental stages and myoblast/myocytes at late stages, highlighting their critical roles in the developing spine. Our work provides insights into the developmental biology of the human spine and the pathogenesis of spine malformation.
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Affiliation(s)
- Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hengqiang Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Lina Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xi Cheng
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zhifa Zheng
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Mengfan Wu
- Institute of Evolution & Marine Biodiversity, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Wen Wen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Shengru Wang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zixiang Zhou
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Haibo Xie
- Institute of Evolution & Marine Biodiversity, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Dengfeng Ruan
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining, 314400, China
| | - Qing Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xinquan Liu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Chengzhu Ou
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Guozhuang Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zhengye Zhao
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Guilin Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yuchen Niu
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiangjie Yin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yuhong Hu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xiaochen Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Wanlu Liu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining, 314400, China
| | - Chengtian Zhao
- Institute of Evolution & Marine Biodiversity, College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Zhihong Wu
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
- Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.
| | - Jianguo Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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Bahmani M, Juhász A, Bose U, Nye-Wood MG, Blundell M, Howitt CA, Colgrave ML. From grain to malt: Tracking changes of ultra-low-gluten barley storage proteins after malting. Food Chem 2024; 432:137189. [PMID: 37619393 DOI: 10.1016/j.foodchem.2023.137189] [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: 02/24/2023] [Revised: 07/25/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023]
Abstract
Barley (Hordeum vulgare L.) is a major cereal crop produced globally. Hordeins, the major storage proteins in barley, can trigger immune responses leading to celiac disease or symptoms associated with food allergy. Here, proteomics approaches were employed to investigate the proteome level changes of grain and malt from the malting barley cultivar, Sloop, and single-, double- and triple hordein-reduced lines. The triple hordein-reduced line is an ultra-low gluten barley cultivar, Kebari®. Using discovery proteomics, 2,688 and 3,034 proteins in the barley and malt samples were detected respectively. Through the application of targeted proteomics, a significant reduction in the quantity of B-, D-, and γ-hordeins, as well as avenin-like proteins, was observed in the ultra-low gluten malt sample. A compensation mechanism was observed evidenced by increased biosynthesis of seed storage globulins, specifically vicilin-like globulins. Overall, this study has provided insights into protein compositional changes after malting in celiac-friendly barley varieties.
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Affiliation(s)
- Mahya Bahmani
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, School of Science, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Angéla Juhász
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, School of Science, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Utpal Bose
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, School of Science, 270 Joondalup Dr, Joondalup, WA 6027, Australia; CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia
| | - Mitchell G Nye-Wood
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, School of Science, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | | | | | - Michelle L Colgrave
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, School of Science, 270 Joondalup Dr, Joondalup, WA 6027, Australia; CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia.
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Kauffenstein G, Martin L, Le Saux O. The Purinergic Nature of Pseudoxanthoma Elasticum. BIOLOGY 2024; 13:74. [PMID: 38392293 PMCID: PMC10886499 DOI: 10.3390/biology13020074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/13/2024] [Accepted: 01/19/2024] [Indexed: 02/24/2024]
Abstract
Pseudoxanthoma Elasticum (PXE) is an inherited disease characterized by elastic fiber calcification in the eyes, the skin and the cardiovascular system. PXE results from mutations in ABCC6 that encodes an ABC transporter primarily expressed in the liver and kidneys. It took nearly 15 years after identifying the gene to better understand the etiology of PXE. ABCC6 function facilitates the efflux of ATP, which is sequentially hydrolyzed by the ectonucleotidases ENPP1 and CD73 into pyrophosphate (PPi) and adenosine, both inhibitors of calcification. PXE, together with General Arterial Calcification of Infancy (GACI caused by ENPP1 mutations) as well as Calcification of Joints and Arteries (CALJA caused by NT5E/CD73 mutations), forms a disease continuum with overlapping phenotypes and shares steps of the same molecular pathway. The explanation of these phenotypes place ABCC6 as an upstream regulator of a purinergic pathway (ABCC6 → ENPP1 → CD73 → TNAP) that notably inhibits mineralization by maintaining a physiological Pi/PPi ratio in connective tissues. Based on a review of the literature and our recent experimental data, we suggest that PXE (and GACI/CALJA) be considered as an authentic "purinergic disease". In this article, we recapitulate the pathobiology of PXE and review molecular and physiological data showing that, beyond PPi deficiency and ectopic calcification, PXE is associated with wide and complex alterations of purinergic systems. Finally, we speculate on the future prospects regarding purinergic signaling and other aspects of this disease.
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Affiliation(s)
- Gilles Kauffenstein
- UMR INSERM 1260, Regenerative Nanomedicine, University of Strasbourg, 67084 Strasbourg, France
| | - Ludovic Martin
- PXE Consultation Center, MAGEC Nord Reference Center for Rare Skin Diseases, Angers University Hospital, 49000 Angers, France
- MITOVASC-UMR CNRS 6015 INSERM 1083, University of Angers, 49000 Angers, France
| | - Olivier Le Saux
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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Geiseler SJ, Hadzic A, Lambertus M, Forbord KM, Sajedi G, Liesz A, Morland C. L-Lactate Treatment at 24 h and 48 h after Acute Experimental Stroke Is Neuroprotective via Activation of the L-Lactate Receptor HCA 1. Int J Mol Sci 2024; 25:1232. [PMID: 38279234 PMCID: PMC10816130 DOI: 10.3390/ijms25021232] [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: 12/22/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 01/28/2024] Open
Abstract
Stroke is the main cause for acquired disabilities. Pharmaceutical or mechanical removal of the thrombus is the cornerstone of stroke treatment but can only be administered to a subset of patients and within a narrow time window. Novel treatment options are therefore required. Here we induced stroke by permanent occlusion of the distal medial cerebral artery of wild-type mice and knockout mice for the lactate receptor hydroxycarboxylic acid receptor 1 (HCA1). At 24 h and 48 h after stroke induction, we injected L-lactate intraperitoneal. The resulting atrophy was measured in Nissl-stained brain sections, and capillary density and neurogenesis were measured after immunolabeling and confocal imaging. In wild-type mice, L-lactate treatment resulted in an HCA1-dependent reduction in the lesion volume accompanied by enhanced angiogenesis. In HCA1 knockout mice, on the other hand, there was no increase in angiogenesis and no reduction in lesion volume in response to L-lactate treatment. Nevertheless, the lesion volumes in HCA1 knockout mice-regardless of L-lactate treatment-were smaller than in control mice, indicating a multifactorial role of HCA1 in stroke. Our findings suggest that L-lactate administered 24 h and 48 h after stroke is protective in stroke. This represents a time window where no effective treatment options are currently available.
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Affiliation(s)
- Samuel J. Geiseler
- Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, 0316 Oslo, Norway; (A.H.); (M.L.); (K.M.F.); (G.S.)
| | - Alena Hadzic
- Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, 0316 Oslo, Norway; (A.H.); (M.L.); (K.M.F.); (G.S.)
| | - Marvin Lambertus
- Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, 0316 Oslo, Norway; (A.H.); (M.L.); (K.M.F.); (G.S.)
| | - Karl Martin Forbord
- Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, 0316 Oslo, Norway; (A.H.); (M.L.); (K.M.F.); (G.S.)
| | - Ghazal Sajedi
- Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, 0316 Oslo, Norway; (A.H.); (M.L.); (K.M.F.); (G.S.)
| | - Arthur Liesz
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians University Munich, 81377 Munich, Germany;
- Graduate School of Systemic Neurosciences Munich, 82152 Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
| | - Cecilie Morland
- Section for Pharmacology and Pharmaceutical Biosciences, Department of Pharmacy, University of Oslo, 0316 Oslo, Norway; (A.H.); (M.L.); (K.M.F.); (G.S.)
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Smeir M, Chumala P, Katselis GS, Liu L. Lymphocyte-Specific Protein 1 Regulates Expression and Stability of Endothelial Nitric Oxide Synthase. Biomolecules 2024; 14:111. [PMID: 38254711 PMCID: PMC10813790 DOI: 10.3390/biom14010111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/14/2023] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
Nitric oxide (NO), synthesized by endothelial nitric oxide synthase (eNOS), plays a critical role in blood pressure regulation. Genome-wide association studies have identified genetic susceptibility loci for hypertension in human lymphocyte-specific protein 1 (LSP1) gene. LSP1 is recognized as modulator of leukocyte extravasation, and endothelial permeability, however, the role of LSP1 in regulation of NO signaling within endothelial cells (ECs) remains unknown. The present study investigated the role of LSP1 in the regulation of eNOS expression and activity utilizing human macrovascular ECs in vitro and LSP1 knockout (KO) mice. In ECs, specific CRISPR-Cas9 genomic editing deleted LSP1 and caused downregulation of eNOS expression. LSP1 gain-of-function through adenovirus-mediated gene transfer was associated with enhanced expression of eNOS. Co-immunoprecipitation and confocal fluorescence microscopy revealed that eNOS and LSP1 formed a protein complex under basal conditions in ECs. Furthermore, LSP1 deficiency in mice promoted significant upregulation and instability of eNOS. Utilizing a mass-spectrometry-based bottom-up proteomics approach, we identified novel truncated forms of eNOS in immunoprecipitates from LSP1 KO aortae. Our experimental data suggest an important role of endothelial LSP1 in regulation of eNOS expression and activity within human ECs and murine vascular tissues.
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Affiliation(s)
- Musstafa Smeir
- Department of Anatomy, Physiology and Pharmacology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada;
| | - Paulos Chumala
- Department of Medicine, Canadian Center for Rural and Agricultural Health, University of Saskatchewan, Saskatoon, SK S7N 2Z4, Canada; (P.C.); (G.S.K.)
| | - George S. Katselis
- Department of Medicine, Canadian Center for Rural and Agricultural Health, University of Saskatchewan, Saskatoon, SK S7N 2Z4, Canada; (P.C.); (G.S.K.)
| | - Lixin Liu
- Department of Anatomy, Physiology and Pharmacology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada;
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Ramli, Aramaki T, Watanabe M, Kondo S. Piezo1 mutant zebrafish as a model of idiopathic scoliosis. Front Genet 2024; 14:1321379. [PMID: 38259612 PMCID: PMC10801085 DOI: 10.3389/fgene.2023.1321379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Scoliosis is a condition where the spine curves sideways, unique to humans due to their upright posture. However, the cause of this disease is not well understood because it is challenging to find a model for experimentation. This study aimed to create a model for human idiopathic scoliosis by manipulating the function of mechanosensitive channels called Piezo channels in zebrafish. Zebrafish were chosen because they experience similar biomechanical forces to humans, particularly in relation to the role of mechanical force in scoliosis progression. Here we describe piezo1 and piezo2a are involved in bone formation, with a double knockout resulting in congenital systemic malformations. However, an in-frame mutation of piezo1 led to fully penetrant juvenile-onset scoliosis, bone asymmetry, reduced tissue mineral density, and abnormal intervertebral discs-resembling non-congenital scoliosis symptoms in humans. These findings suggest that functional Piezo channels responding to mechanical forces are crucial for bone formation and maintaining spine integrity, providing insights into skeletal disorders.
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Affiliation(s)
- Ramli
- Laboratory of Pattern Formation, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Toshihiro Aramaki
- Laboratory of Pattern Formation, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Japan Science and Technology Agency, PRESTO, Tokyo, Japan
| | - Masakatsu Watanabe
- Laboratory of Pattern Formation, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Shigeru Kondo
- Laboratory of Pattern Formation, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
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Derrick CJ, Szenker-Ravi E, Santos-Ledo A, Alqahtani A, Yusof A, Eley L, Coleman AHL, Tohari S, Ng AYJ, Venkatesh B, Alharby E, Mansard L, Bonnet-Dupeyron MN, Roux AF, Vaché C, Roume J, Bouvagnet P, Almontashiri NAM, Henderson DJ, Reversade B, Chaudhry B. Functional analysis of germline VANGL2 variants using rescue assays of vangl2 knockout zebrafish. Hum Mol Genet 2024; 33:150-169. [PMID: 37815931 PMCID: PMC10772043 DOI: 10.1093/hmg/ddad171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/11/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023] Open
Abstract
Developmental studies have shown that the evolutionarily conserved Wnt Planar Cell Polarity (PCP) pathway is essential for the development of a diverse range of tissues and organs including the brain, spinal cord, heart and sensory organs, as well as establishment of the left-right body axis. Germline mutations in the highly conserved PCP gene VANGL2 in humans have only been associated with central nervous system malformations, and functional testing to understand variant impact has not been performed. Here we report three new families with missense variants in VANGL2 associated with heterotaxy and congenital heart disease p.(Arg169His), non-syndromic hearing loss p.(Glu465Ala) and congenital heart disease with brain defects p.(Arg135Trp). To test the in vivo impact of these and previously described variants, we have established clinically-relevant assays using mRNA rescue of the vangl2 mutant zebrafish. We show that all variants disrupt Vangl2 function, although to different extents and depending on the developmental process. We also begin to identify that different VANGL2 missense variants may be haploinsufficient and discuss evidence in support of pathogenicity. Together, this study demonstrates that zebrafish present a suitable pipeline to investigate variants of unknown significance and suggests new avenues for investigation of the different developmental contexts of VANGL2 function that are clinically meaningful.
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Affiliation(s)
- Christopher J Derrick
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | | | - Adrian Santos-Ledo
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Ahlam Alqahtani
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Amirah Yusof
- Genome Institute of Singapore (GIS), A*STAR, 60 Biopolis St, 138672, Singapore
| | - Lorraine Eley
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Alistair H L Coleman
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Sumanty Tohari
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Dr, Proteos, 138673, Singapore
| | - Alvin Yu-Jin Ng
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Dr, Proteos, 138673, Singapore
- MGI Tech Singapore Pte Ltd, 21 Biopolis Rd, 138567, Singapore
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Dr, Proteos, 138673, Singapore
| | - Essa Alharby
- Center for Genetics and Inherited Diseases, Taibah University, 7534 Abdul Muhsin Ibn Abdul Aziz, Al Ihn, Al-Madinah al-Munawwarah 42318, Saudi Arabia
- Faculty of Applied Medical Sciences, Taibah University, Janadah Bin Umayyah Road, Tayba, Al-Madinah al-Munawwarah 42353, Saudi Arabia
| | - Luke Mansard
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, 80 Av. Augustin Fliche, 34000 Montpellier, France
| | | | - Anne-Francoise Roux
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, 80 Av. Augustin Fliche, 34000 Montpellier, France
| | - Christel Vaché
- Molecular Genetics Laboratory, University of Montpellier, CHU Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, 80 Av. Augustin Fliche, 34000 Montpellier, France
| | - Joëlle Roume
- Département de Génétique, CHI Poissy, St Germain-en-Laye, 10 Rue du Champ Gaillard, 78300 Poissy, France
| | - Patrice Bouvagnet
- CPDPN, Hôpital MFME, CHU de Martinique, Fort de France, Fort-de-France 97261, Martinique, France
| | - Naif A M Almontashiri
- Center for Genetics and Inherited Diseases, Taibah University, 7534 Abdul Muhsin Ibn Abdul Aziz, Al Ihn, Al-Madinah al-Munawwarah 42318, Saudi Arabia
- Faculty of Applied Medical Sciences, Taibah University, Janadah Bin Umayyah Road, Tayba, Al-Madinah al-Munawwarah 42353, Saudi Arabia
| | - Deborah J Henderson
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Bruno Reversade
- Genome Institute of Singapore (GIS), A*STAR, 60 Biopolis St, 138672, Singapore
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Dr, Proteos, 138673, Singapore
- Smart-Health Initiative, BESE, KAUST, Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Medical Genetics Department, Koç Hospital Davutpaşa Caddesi 34010 Topkapı Istanbul, Istanbul, Turkey
| | - Bill Chaudhry
- Biosciences Institute, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, United Kingdom
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Ortega LA, Aragon-Carvajal DM, Cortes-Corso KT, Forero-Castillo F. Early developmental risks for tobacco addiction: A probabilistic epigenesis framework. Neurosci Biobehav Rev 2024; 156:105499. [PMID: 38056543 DOI: 10.1016/j.neubiorev.2023.105499] [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: 07/03/2023] [Revised: 11/23/2023] [Accepted: 12/01/2023] [Indexed: 12/08/2023]
Abstract
Considerable progress has been made in elucidating the relationships between early life psychobiological and environmental risk factors and the development of tobacco addiction. However, a comprehensive understanding of the heterogeneity in tobacco addiction phenotypes requires integrating research findings. The probabilistic epigenesis meta-theory offers a valuable framework for this integration, considering systemic, multilevel, developmental, and evolutionary perspectives. In this paper, we critically review relevant research on early developmental risks associated with tobacco addiction and highlight the integrative heuristic value of the probabilistic epigenesis framework for this research. For this, we propose a four-level systems approach as an initial step towards integration, analyzing complex interactions among different levels of influence. Additionally, we explore a coaction approach to examine key interactions between early risk factors. Moreover, we introduce developmental pathways to understand interindividual differences in tobacco addiction risk during development. This integrative approach holds promise for advancing our understanding of tobacco addiction etiology and informing potentially effective intervention strategies.
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Affiliation(s)
- Leonardo A Ortega
- Facultad de Psicologia, Fundacion Universitaria Konrad Lorenz, Colombia.
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Torraca V, White RJ, Sealy IM, Mazon-Moya M, Duggan G, Willis AR, Busch-Nentwich EM, Mostowy S. Transcriptional profiling of zebrafish identifies host factors controlling susceptibility to Shigella flexneri. Dis Model Mech 2024; 17:dmm050431. [PMID: 38131137 PMCID: PMC10846535 DOI: 10.1242/dmm.050431] [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: 08/08/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023] Open
Abstract
Shigella flexneri is a human-adapted pathovar of Escherichia coli that can invade the intestinal epithelium, causing inflammation and bacillary dysentery. Although an important human pathogen, the host response to S. flexneri has not been fully described. Zebrafish larvae represent a valuable model for studying human infections in vivo. Here, we use a Shigella-zebrafish infection model to generate mRNA expression profiles of host response to Shigella infection at the whole-animal level. Immune response-related processes dominate the signature of early Shigella infection (6 h post-infection). Consistent with its clearance from the host, the signature of late Shigella infection (24 h post-infection) is significantly changed, and only a small set of immune-related genes remain differentially expressed, including acod1 and gpr84. Using mutant lines generated by ENU, CRISPR mutagenesis and F0 crispants, we show that acod1- and gpr84-deficient larvae are more susceptible to Shigella infection. Together, these results highlight the power of zebrafish to model infection by bacterial pathogens and reveal the mRNA expression of the early (acutely infected) and late (clearing) host response to Shigella infection.
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Affiliation(s)
- Vincenzo Torraca
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
- School of Life Sciences, University of Westminster, London W1W 6UW, UK
| | - Richard J. White
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK
- School of Biological and Behavioural Sciences, Faculty of Science and Engineering, Queen Mary University of London, London E1 4NS, UK
| | - Ian M. Sealy
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK
- School of Biological and Behavioural Sciences, Faculty of Science and Engineering, Queen Mary University of London, London E1 4NS, UK
| | - Maria Mazon-Moya
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Gina Duggan
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Alexandra R. Willis
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Elisabeth M. Busch-Nentwich
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK
- School of Biological and Behavioural Sciences, Faculty of Science and Engineering, Queen Mary University of London, London E1 4NS, UK
| | - Serge Mostowy
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
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