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Wiese J, Richards E, Kowalko JE, McGaugh SE. Loci associated with cave-derived traits concentrate in specific regions of the Mexican cavefish genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.587360. [PMID: 38585759 PMCID: PMC10996652 DOI: 10.1101/2024.03.29.587360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
A major goal of modern evolutionary biology is connecting phenotypic evolution with its underlying genetic basis. The Mexican cavefish (Astyanax mexicanus), a characin fish species comprised of a surface ecotype and a cave-derived ecotype, is well suited as a model to study the genetic mechanisms underlying adaptation to extreme environments. Here we map 206 previously published quantitative trait loci (QTL) for cave-derived traits in A. mexicanus to the newest version of the surface fish genome assembly, AstMex3. This analysis revealed that QTL cluster in the genome more than expected by chance, and this clustering is not explained by the distribution of genes in the genome. To investigate whether certain characteristics of the genome facilitate phenotypic evolution, we tested whether genomic characteristics, such as highly mutagenic CpG sites, are reliable predictors of the sites of trait evolution but did not find any significant trends. Finally, we combined the QTL map with previously collected expression and selection data to identify a list of 36 candidate genes that may underlie the repeated evolution of cave phenotypes, including rgrb which is predicted to be involved in phototransduction. We found this gene has disrupted exons in all non-hybrid cave populations but intact reading frames in surface fish. Overall, our results suggest specific "evolutionary hotspots" in the genome may play significant roles in driving adaptation to the cave environment in Astyanax mexicanus and demonstrate how this compiled dataset can facilitate our understanding of the genetic basis of repeated evolution in the Mexican cavefish.
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Affiliation(s)
- Jonathan Wiese
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
| | - Emilie Richards
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
| | | | - Suzanne E McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
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2
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Hu S, Hang X, Wei Y, Wang H, Zhang L, Zhao L. Crosstalk among podocytes, glomerular endothelial cells and mesangial cells in diabetic kidney disease: an updated review. Cell Commun Signal 2024; 22:136. [PMID: 38374141 PMCID: PMC10875896 DOI: 10.1186/s12964-024-01502-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 01/28/2024] [Indexed: 02/21/2024] Open
Abstract
Diabetic kidney disease (DKD) is a long-term and serious complication of diabetes that affects millions of people worldwide. It is characterized by proteinuria, glomerular damage, and renal fibrosis, leading to end-stage renal disease, and the pathogenesis is complex and involves multiple cellular and molecular mechanisms. Among three kinds of intraglomerular cells including podocytes, glomerular endothelial cells (GECs) and mesangial cells (MCs), the alterations in one cell type can produce changes in the others. The cell-to-cell crosstalk plays a crucial role in maintaining the glomerular filtration barrier (GFB) and homeostasis. In this review, we summarized the recent advances in understanding the pathological changes and interactions of these three types of cells in DKD and then focused on the signaling pathways and factors that mediate the crosstalk, such as angiopoietins, vascular endothelial growth factors, transforming growth factor-β, Krüppel-like factors, retinoic acid receptor response protein 1 and exosomes, etc. Furthermore, we also simply introduce the application of the latest technologies in studying cell interactions within glomerular cells and new promising mediators for cell crosstalk in DKD. In conclusion, this review provides a comprehensive and updated overview of the glomerular crosstalk in DKD and highlights its importance for the development of novel intervention approaches.
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Affiliation(s)
- Shiwan Hu
- Institute of Metabolic Diseases, Guang' anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China
- Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xing Hang
- Institute of Metabolic Diseases, Guang' anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China
- Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Yu Wei
- Institute of Metabolic Diseases, Guang' anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China
- Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Han Wang
- Beijing University of Chinese Medicine, Beijing, 100029, China.
| | - Lili Zhang
- Institute of Metabolic Diseases, Guang' anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China.
| | - Linhua Zhao
- Institute of Metabolic Diseases, Guang' anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China.
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3
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Ibarra-Soria X, Thierion E, Mok GF, Münsterberg AE, Odom DT, Marioni JC. A transcriptional and regulatory map of mouse somite maturation. Dev Cell 2023; 58:1983-1995.e7. [PMID: 37499658 PMCID: PMC10563765 DOI: 10.1016/j.devcel.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/12/2023] [Accepted: 07/04/2023] [Indexed: 07/29/2023]
Abstract
The mammalian body plan is shaped by rhythmic segmentation of mesoderm into somites, which are transient embryonic structures that form down each side of the neural tube. We have analyzed the genome-wide transcriptional and chromatin dynamics occurring within nascent somites, from early inception of somitogenesis to the latest stages of body plan establishment. We created matched gene expression and open chromatin maps for the three leading pairs of somites at six time points during mouse embryonic development. We show that the rate of somite differentiation accelerates as development progresses. We identified a conserved maturation program followed by all somites, but somites from more developed embryos concomitantly switch on differentiation programs from derivative cell lineages soon after segmentation. Integrated analysis of the somitic transcriptional and chromatin activities identified opposing regulatory modules controlling the onset of differentiation. Our results provide a powerful, high-resolution view of the molecular genetics underlying somitic development in mammals.
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Affiliation(s)
- Ximena Ibarra-Soria
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.
| | - Elodie Thierion
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Gi Fay Mok
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Andrea E Münsterberg
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Duncan T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK; DKFZ, Division of Regulatory Genomics and Cancer Evolution B270, Im Neunheimer Feld 280, Heidelberg, 69120, Germany.
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge CB10 1SD, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
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Pierro JD, Ahir BK, Baker NC, Kleinstreuer NC, Xia M, Knudsen TB. Computational model for fetal skeletal defects potentially linked to disruption of retinoic acid signaling. Front Pharmacol 2022; 13:971296. [PMID: 36172177 PMCID: PMC9511990 DOI: 10.3389/fphar.2022.971296] [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: 06/16/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
All-trans retinoic acid (ATRA) gradients determine skeletal patterning morphogenesis and can be disrupted by diverse genetic or environmental factors during pregnancy, leading to fetal skeleton defects. Adverse Outcome Pathway (AOP) frameworks for ATRA metabolism, signaling, and homeostasis allow for the development of new approach methods (NAMs) for predictive toxicology with less reliance on animal testing. Here, a data-driven model was constructed to identify chemicals associated with both ATRA pathway bioactivity and prenatal skeletal defects. The phenotype data was culled from ToxRefDB prenatal developmental toxicity studies and produced a list of 363 ToxRefDB chemicals with altered skeletal observations. Defects were classified regionally as cranial, post-cranial axial, appendicular, and other (unspecified) features based on ToxRefDB descriptors. To build a multivariate statistical model, high-throughput screening bioactivity data from >8,070 chemicals in ToxCast/Tox21 across 10 in vitro assays relevant to the retinoid signaling system were evaluated and compared to literature-based candidate reference chemicals in the dataset. There were 48 chemicals identified for effects on both in vivo skeletal defects and in vitro ATRA pathway targets for computational modeling. The list included 28 chemicals with prior evidence of skeletal defects linked to retinoid toxicity and 20 chemicals without prior evidence. The combination of thoracic cage defects and DR5 (direct repeats of 5 nucleotides for RAR/RXR transactivation) disruption was the most frequently occurring phenotypic and target disturbance, respectively. This data model provides valuable AOP elucidation and validates current mechanistic understanding. These findings also shed light on potential avenues for new mechanistic discoveries related to ATRA pathway disruption and associated skeletal dysmorphogenesis due to environmental exposures.
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Affiliation(s)
- Jocylin D. Pierro
- Center for Computational Toxicology and Exposure (CCTE), Computational Toxicology and Bioinformatics Branch (CTBB), Office of Research and Development (ORD), U.S. Environmental Protection Agency (USEPA), Research Triangle Park, NC, United States
| | - Bhavesh K. Ahir
- Eurofins Medical Device Testing, Lancaster, PA, United States
| | - Nancy C. Baker
- Scientific Computing and Data Curation Division (SCDCD), Leidos Contractor, Center for Computational Toxicology and Exposure (CCTE), USEPA/ORD, Research Triangle Park, NC, United States
| | - Nicole C. Kleinstreuer
- Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM), National Toxicology Program, National Institutes of Health, Research Triangle Park, NC, United States
| | - Menghang Xia
- Division for Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Thomas B. Knudsen
- Center for Computational Toxicology and Exposure (CCTE), Computational Toxicology and Bioinformatics Branch (CTBB), Office of Research and Development (ORD), U.S. Environmental Protection Agency (USEPA), Research Triangle Park, NC, United States
- *Correspondence: Thomas B. Knudsen, , orcid.org/0000-0002-5036-596x
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Rodrigues BM, Mathias LS, Deprá IDC, Cury SS, de Oliveira M, Olimpio RMC, De Sibio MT, Gonçalves BM, Nogueira CR. Effects of Triiodothyronine on Human Osteoblast-Like Cells: Novel Insights From a Global Transcriptome Analysis. Front Cell Dev Biol 2022; 10:886136. [PMID: 35784485 PMCID: PMC9248766 DOI: 10.3389/fcell.2022.886136] [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: 02/28/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Thyroid hormones play a significant role in bone development and maintenance, with triiodothyronine (T3) particularly being an important modulator of osteoblast differentiation, proliferation, and maintenance. However, details of the biological processes (BPs) and molecular pathways affected by T3 in osteoblasts remain unclear.Methods: To address this issue, primary cultures of human adipose-derived mesenchymal stem cells were subjected to our previously established osteoinduction protocol, and the resultant osteoblast-like cells were treated with 1 nm or 10 nm T3 for 72 h. RNA sequencing (RNA-Seq) was performed using the Illumina platform, and differentially expressed genes (DEGs) were identified from the raw data using Kallisto and DESeq2. Enrichment analysis of DEGs was performed against the Gene Ontology Consortium database for BP terms using the R package clusterProfiler and protein network analysis by STRING.Results: Approximately 16,300 genes were analyzed by RNA-Seq, with 343 DEGs regulated in the 1 nm T3 group and 467 upregulated in the 10 nm T3 group. Several independent BP terms related to bone metabolism were significantly enriched, with a number of genes shared among them (FGFR2, WNT5A, WNT3, ROR2, VEGFA, FBLN1, S1PR1, PRKCZ, TGFB3, and OSR1 for 1nM T3; and FZD1, SMAD6, NOG, NEO1, and ENG for 10 nm T3). An osteoblast-related search in the literature regarding this set of genes suggests that both T3 doses are unfavorable for osteoblast development, mainly hindering BMP and canonical and non-canonical WNT signaling.Conclusions: Therefore, this study provides new directions toward the elucidation of the mechanisms of T3 action on osteoblast metabolism, with potential future implications for the treatment of endocrine-related bone pathologies.
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Affiliation(s)
- Bruna Moretto Rodrigues
- Department of Internal Medicine, Medical School Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
| | - Lucas Solla Mathias
- Department of Internal Medicine, Medical School Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
| | - Igor de Carvalho Deprá
- Department of Internal Medicine, Medical School Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
| | - Sarah Santiloni Cury
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, Brazil
| | - Miriane de Oliveira
- Department of Internal Medicine, Medical School Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
| | | | - Maria Teresa De Sibio
- Department of Internal Medicine, Medical School Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
| | - Bianca Mariani Gonçalves
- Department of Internal Medicine, Medical School Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
| | - Célia Regina Nogueira
- Department of Internal Medicine, Medical School Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
- *Correspondence: Célia Regina Nogueira,
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Gur M, Edri T, Moody SA, Fainsod A. Retinoic Acid is Required for Normal Morphogenetic Movements During Gastrulation. Front Cell Dev Biol 2022; 10:857230. [PMID: 35531100 PMCID: PMC9068879 DOI: 10.3389/fcell.2022.857230] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/21/2022] [Indexed: 11/23/2022] Open
Abstract
Retinoic acid (RA) is a central regulatory signal that controls numerous developmental processes in vertebrate embryos. Although activation of Hox expression is considered one of the earliest functions of RA signaling in the embryo, there is evidence that embryos are poised to initiate RA signaling just before gastrulation begins, and manipulations of the RA pathway have been reported to show gastrulation defects. However, which aspects of gastrulation are affected have not been explored in detail. We previously showed that partial inhibition of RA biosynthesis causes a delay in the rostral migration of some of the earliest involuting cells, the leading edge mesendoderm (LEM) and the prechordal mesoderm (PCM). Here we identify several detrimental gastrulation defects resulting from inhibiting RA biosynthesis by three different treatments. RA reduction causes a delay in the progression through gastrulation as well as the rostral migration of the goosecoid-positive PCM cells. RA inhibition also hampered the elongation of explanted dorsal marginal zones, the compaction of the blastocoel, and the length of Brachet’s cleft, all of which indicate an effect on LEM/PCM migration. The cellular mechanisms underlying this deficit were shown to include a reduced deposition of fibronectin along Brachet’s cleft, the substrate for their migration, as well as impaired separation of the blastocoel roof and involuting mesoderm, which is important for the formation of Brachet’s cleft and successful LEM/PCM migration. We further show reduced non-canonical Wnt signaling activity and altered expression of genes in the Ephrin and PDGF signaling pathways, both of which are required for the rostral migration of the LEM/PCM, following RA reduction. Together, these experiments demonstrate that RA signaling performs a very early function critical for the progression of gastrulation morphogenetic movements.
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Affiliation(s)
- Michal Gur
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tamir Edri
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sally A. Moody
- Department of Anatomy and Cell Biology, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States
- *Correspondence: Sally A. Moody, ; Abraham Fainsod,
| | - Abraham Fainsod
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- *Correspondence: Sally A. Moody, ; Abraham Fainsod,
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Gur M, Bendelac-Kapon L, Shabtai Y, Pillemer G, Fainsod A. Reduced Retinoic Acid Signaling During Gastrulation Induces Developmental Microcephaly. Front Cell Dev Biol 2022; 10:844619. [PMID: 35372345 PMCID: PMC8967241 DOI: 10.3389/fcell.2022.844619] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/24/2022] [Indexed: 12/21/2022] Open
Abstract
Retinoic acid (RA) is a central signaling molecule regulating multiple developmental decisions during embryogenesis. Excess RA induces head malformations, primarily by expansion of posterior brain structures at the expense of anterior head regions, i.e., hindbrain expansion. Despite this extensively studied RA teratogenic effect, a number of syndromes exhibiting microcephaly, such as DiGeorge, Vitamin A Deficiency, Fetal Alcohol Syndrome, and others, have been attributed to reduced RA signaling. This causative link suggests a requirement for RA signaling during normal head development in all these syndromes. To characterize this novel RA function, we studied the involvement of RA in the early events leading to head formation in Xenopus embryos. This effect was mapped to the earliest RA biosynthesis in the embryo within the gastrula Spemann-Mangold organizer. Head malformations were observed when reduced RA signaling was induced in the endogenous Spemann-Mangold organizer and in the ectopic organizer of twinned embryos. Two embryonic retinaldehyde dehydrogenases, ALDH1A2 (RALDH2) and ALDH1A3 (RALDH3) are initially expressed in the organizer and subsequently mark the trunk and the migrating leading edge mesendoderm, respectively. Gene-specific knockdowns and CRISPR/Cas9 targeting show that RALDH3 is a key enzyme involved in RA production required for head formation. These observations indicate that in addition to the teratogenic effect of excess RA on head development, RA signaling also has a positive and required regulatory role in the early formation of the head during gastrula stages. These results identify a novel RA activity that concurs with its proposed reduction in syndromes exhibiting microcephaly.
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Wu H, Zhao D, Wang C, Zhang D, Tang M, Qian S, Xu L, Xia T, Zhou J, Wang G, He Y, Gao L, Chen W, Li L, Yang W, Zhao Q, Hu C, Hu A. All-Trans Retinoic Acid Prevents the Progression of Gastric Precancerous Lesions by Regulating Disordered Retinoic Acid Metabolism. Nutr Cancer 2022; 74:3351-3362. [PMID: 35225106 DOI: 10.1080/01635581.2022.2044062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Hanhan Wu
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Didi Zhao
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Chen Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Daoming Zhang
- Department of Gastroenterology, Lujiang County People’s Hospital, Hefei, Anhui, PR China
| | - Min Tang
- Department of Gastroenterology and Hepatology, the Fourth Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Shiqing Qian
- Department of Pathology, Lujiang County People’s Hospital, Hefei, Anhui, PR China
| | - Lina Xu
- Department of Gastroenterology, Lujiang County People’s Hospital, Hefei, Anhui, PR China
| | - Tao Xia
- Department of Gastroenterology, Lujiang County People’s Hospital, Hefei, Anhui, PR China
| | - Juanyan Zhou
- Department of Gastroenterology and Hepatology, the Fourth Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Guangjun Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Yue He
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Lei Gao
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Wenjun Chen
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Li Li
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Wanshui Yang
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Qihong Zhao
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Chuanlai Hu
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Anla Hu
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
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9
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Enhanced Loss of Retinoic Acid Network Genes in Xenopus laevis Achieves a Tighter Signal Regulation. Cells 2022; 11:cells11030327. [PMID: 35159137 PMCID: PMC8834563 DOI: 10.3390/cells11030327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 12/10/2022] Open
Abstract
Retinoic acid (RA) is a major regulatory signal during embryogenesis produced from vitamin A (retinol) by an extensive, autoregulating metabolic and signaling network to prevent fluctuations that result in developmental malformations. Xenopus laevis is an allotetraploid hybrid frog species whose genome includes L (long) and S (short) chromosomes from the originating species. Evolutionarily, the X. laevis subgenomes have been losing either L or S homoeologs in about 43% of genes to generate singletons. In the RA network, out of the 47 genes, about 47% have lost one of the homoeologs, like the genome average. Interestingly, RA metabolism genes from storage (retinyl esters) to retinaldehyde production exhibit enhanced gene loss with 75% singletons out of 28 genes. The effect of this gene loss on RA signaling autoregulation was studied. Employing transient RA manipulations, homoeolog gene pairs were identified in which one homoeolog exhibits enhanced responses or looser regulation than the other, while in other pairs both homoeologs exhibit similar RA responses. CRISPR/Cas9 targeting of individual homoeologs to reduce their activity supports the hypothesis where the RA metabolic network gene loss results in tighter network regulation and more efficient RA robustness responses to overcome complex regulation conditions.
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Vogiatzi A, Baltsavia I, Dialynas E, Theodorou V, Zhou Y, Deligianni E, Iliopoulos I, Wilkie AOM, Twigg SRF, Mavrothalassitis G. Erf Affects Commitment and Differentiation of Osteoprogenitor Cells in Cranial Sutures via the Retinoic Acid Pathway. Mol Cell Biol 2021; 41:e0014921. [PMID: 33972395 PMCID: PMC8300784 DOI: 10.1128/mcb.00149-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/22/2021] [Accepted: 04/29/2021] [Indexed: 12/13/2022] Open
Abstract
ETS2 repressor factor (ERF) haploinsufficiency causes late-onset craniosynostosis (CRS) (OMIM entry 600775; CRS4) in humans, while in mice Erf insufficiency also leads to a similar multisuture synostosis phenotype preceded by mildly reduced calvarium ossification. However, neither the cell types affected nor the effects per se have been identified so far. Here, we establish an ex vivo system for the expansion of suture-derived mesenchymal stem and progenitor cells (sdMSCs) and analyze the role of Erf levels in their differentiation. Cellular data suggest that Erf insufficiency specifically decreases osteogenic differentiation of sdMSCs, resulting in the initially delayed mineralization of the calvarium. Transcriptome analysis indicates that Erf is required for efficient osteogenic lineage commitment of sdMSCs. Elevated retinoic acid catabolism due to increased levels of the cytochrome P450 superfamily member Cyp26b1 as a result of decreased Erf levels appears to be the underlying mechanism leading to defective differentiation. Exogenous addition of retinoic acid can rescue the osteogenic differentiation defect, suggesting that Erf affects cranial bone mineralization during skull development through retinoic acid gradient regulation.
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Affiliation(s)
| | | | | | | | - Yan Zhou
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | | | | | - Andrew O. M. Wilkie
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Stephen R. F. Twigg
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - George Mavrothalassitis
- Medical School, University of Crete, Heraklion, Crete, Greece
- IMBB, FORTH, Heraklion, Crete, Greece
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11
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Williams AL, Bohnsack BL. The Ocular Neural Crest: Specification, Migration, and Then What? Front Cell Dev Biol 2021; 8:595896. [PMID: 33425902 PMCID: PMC7785809 DOI: 10.3389/fcell.2020.595896] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/04/2020] [Indexed: 12/11/2022] Open
Abstract
During vertebrate embryonic development, a population of dorsal neural tube-derived stem cells, termed the neural crest (NC), undergo a series of morphogenetic changes and extensive migration to become a diverse array of cell types. Around the developing eye, this multipotent ocular NC cell population, called the periocular mesenchyme (POM), comprises migratory mesenchymal cells that eventually give rise to many of the elements in the anterior of the eye, such as the cornea, sclera, trabecular meshwork, and iris. Molecular cell biology and genetic analyses of congenital eye diseases have provided important information on the regulation of NC contributions to this area of the eye. Nevertheless, a complete understanding of the NC as a contributor to ocular development remains elusive. In addition, positional information during ocular NC migration and the molecular pathways that regulate end tissue differentiation have yet to be fully elucidated. Further, the clinical challenges of ocular diseases, such as Axenfeld-Rieger syndrome (ARS), Peters anomaly (PA) and primary congenital glaucoma (PCG), strongly suggest the need for better treatments. While several aspects of NC evolution have recently been reviewed, this discussion will consolidate the most recent current knowledge on the specification, migration, and contributions of the NC to ocular development, highlighting the anterior segment and the knowledge obtained from the clinical manifestations of its associated diseases. Ultimately, this knowledge can inform translational discoveries with potential for sorely needed regenerative therapies.
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Affiliation(s)
- Antionette L Williams
- Division of Ophthalmology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, United States
| | - Brenda L Bohnsack
- Division of Ophthalmology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, United States.,Department of Ophthalmology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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12
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Schubert M, Gibert Y. Retinoids in Embryonic Development. Biomolecules 2020; 10:biom10091278. [PMID: 32899684 PMCID: PMC7564826 DOI: 10.3390/biom10091278] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/23/2022] Open
Affiliation(s)
- Michael Schubert
- CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche, Sorbonne Université, 181 Chemin du Lazaret, 06230 Villefranche-sur-Mer, France
- Correspondence: ; Tel.: +33-(0)-4-93-76-37-91
| | - Yann Gibert
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS 39216, USA;
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Song J, Zhao W, Lu C, Shao X. Spliced X-box binding protein 1 induces liver cancer cell death via activating the Mst1-JNK-mROS signalling pathway. J Cell Physiol 2020; 235:9378-9387. [PMID: 32335916 DOI: 10.1002/jcp.29742] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/11/2020] [Accepted: 04/18/2020] [Indexed: 12/18/2022]
Abstract
Previous studies have found that the primary pathogenesis of liver cancer progression is linked to excessive cancer cell proliferation and rapid metastasis. Although therapeutic advances have been made for the treatment of liver cancer, the mechanism underlying the liver cancer progression has not been fully addressed. In the present study, we explored the role of spliced X-box binding protein 1 (XBP1) in regulating the viability and death of liver cancer cells in vitro. Our study demonstrated that XBP1 was upregulated in liver cancer cells when compared to the primary hepatocytes. Interestingly, the deletion of XBP1 could reduce the viability of liver cancer cells in vitro via inducing apoptotic response. Further, we found that XBP1 downregulation was also linked to proliferation arrest and migration inhibition. At the molecular levels, XBP1 inhibition is followed by activation of the Mst1 pathway which promoted the phosphorylation of c-Jun N-terminal kinase (JNK). Then, the active Mst1-JNK pathway mediated mitochondrial reactive oxygen species (mROS) overproduction and then excessive ROS induced cancer cell death. Therefore, our study demonstrated a novel role played by XBP1 in modulating the viability of liver cancer cells via the Mst1-JNK-mROS pathways.
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Affiliation(s)
- Jie Song
- Department of Hepatopancreatobiliary Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Wei Zhao
- Department of Pharmacy, The Second Hospital of Jilin University, Changchun, China
| | - Chang Lu
- Department of Anesthesiology, The Second Hospital of Jilin University, Changchun, China
| | - Xue Shao
- Department of Hepatopancreatobiliary Medicine, The Second Hospital of Jilin University, Changchun, China
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