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Warburton CL, Costilla R, Engle BN, Moore SS, Corbet NJ, Fordyce G, McGowan MR, Burns BM, Hayes BJ. Concurrently mapping quantitative trait loci associations from multiple subspecies within hybrid populations. Heredity (Edinb) 2023; 131:350-360. [PMID: 37798326 PMCID: PMC10673866 DOI: 10.1038/s41437-023-00651-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/07/2023] Open
Abstract
Many of the world's agriculturally important plant and animal populations consist of hybrids of subspecies. Cattle in tropical and sub-tropical regions for example, originate from two subspecies, Bos taurus indicus (Bos indicus) and Bos taurus taurus (Bos taurus). Methods to derive the underlying genetic architecture for these two subspecies are essential to develop accurate genomic predictions in these hybrid populations. We propose a novel method to achieve this. First, we use haplotypes to assign SNP alleles to ancestral subspecies of origin in a multi-breed and multi-subspecies population. Then we use a BayesR framework to allow SNP alleles originating from the different subspecies differing effects. Applying this method in a composite population of B. indicus and B. taurus hybrids, our results show that there are underlying genomic differences between the two subspecies, and these effects are not identified in multi-breed genomic evaluations that do not account for subspecies of origin effects. The method slightly improved the accuracy of genomic prediction. More significantly, by allocating SNP alleles to ancestral subspecies of origin, we were able to identify four SNP with high posterior probabilities of inclusion that have not been previously associated with cattle fertility and were close to genes associated with fertility in other species. These results show that haplotypes can be used to trace subspecies of origin through the genome of this hybrid population and, in conjunction with our novel Bayesian analysis, subspecies SNP allele allocation can be used to increase the accuracy of QTL association mapping in genetically diverse populations.
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Affiliation(s)
- Christie L Warburton
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia.
| | - Roy Costilla
- Agresearch Limited, Ruakura Research Centre, Hamilton, 3214, New Zealand
| | - Bailey N Engle
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia
| | - Stephen S Moore
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia
| | - Nicholas J Corbet
- Formerly Central Queensland University, School of Health, Medical and Applied Sciences, Rockhampton, QLD, Australia
| | - Geoffry Fordyce
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia
| | - Michael R McGowan
- The University of Queensland, School of Veterinary Science, St Lucia, QLD, Australia
| | - Brian M Burns
- Formerly Department of Agriculture and Fisheries, Rockhampton, QLD, Australia
| | - Ben J Hayes
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St. Lucia, QLD, Australia
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Huang R, Zhang C, Zheng Y, Zhang W, Huang H, Qiu M, Li J, Li F. ISL1 regulates lung branching morphogenesis via Shh signaling pathway. J Biol Chem 2023; 299:105034. [PMID: 37442233 PMCID: PMC10406864 DOI: 10.1016/j.jbc.2023.105034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
Lung branching morphogenesis relies on a complex coordination of multiple signaling pathways and transcription factors. Here, we found that ablation of the LIM homeodomain transcription factor Islet1 (Isl1) in lung epithelium resulted in defective branching morphogenesis and incomplete formation of five lobes. A reduction in mesenchymal cell proliferation was observed in Isl1ShhCre lungs. There was no difference in apoptosis between the wild-type (ShhCre) and Isl1ShhCre embryos. RNA-Seq and in situ hybridization analysis showed that Shh, Ptch1, Sox9, Irx1, Irx2, Tbx2, and Tbx3 were downregulated in the lungs of Isl1ShhCre embryos. ChIP assay implied the Shh gene served as a direct target of ISL1, since the transcription factor ISL1 could bind to the Shh epithelial enhancer sequence (MACS1). Also, activation of the Hedgehog pathway via ectopic gene expression rescued the defects caused by Isl1 ablation, confirming the genetic integration of Hedgehog signaling. In conclusion, our works suggest that epithelial Isl1 regulates lung branching morphogenesis through administrating the Shh signaling mediated epithelial-mesenchymal communications.
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Affiliation(s)
- Ruiqi Huang
- Zhejiang Key Laboratory of Organ Development and Regeneration, Institute of Developmental and Regenerative Biology, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, People's Republic of China
| | - Chujing Zhang
- Zhejiang Key Laboratory of Organ Development and Regeneration, Institute of Developmental and Regenerative Biology, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, People's Republic of China
| | - Yuting Zheng
- Zhejiang Key Laboratory of Organ Development and Regeneration, Institute of Developmental and Regenerative Biology, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, People's Republic of China
| | - Wei Zhang
- Zhejiang Key Laboratory of Organ Development and Regeneration, Institute of Developmental and Regenerative Biology, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, People's Republic of China
| | - Huarong Huang
- Zhejiang Key Laboratory of Organ Development and Regeneration, Institute of Developmental and Regenerative Biology, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, People's Republic of China
| | - Mengsheng Qiu
- Zhejiang Key Laboratory of Organ Development and Regeneration, Institute of Developmental and Regenerative Biology, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, People's Republic of China
| | - Jianying Li
- Zhejiang Key Laboratory of Organ Development and Regeneration, Institute of Developmental and Regenerative Biology, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, People's Republic of China.
| | - Feixue Li
- Zhejiang Key Laboratory of Organ Development and Regeneration, Institute of Developmental and Regenerative Biology, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, People's Republic of China.
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Wolf L, Boutros M. The role of Evi/Wntless in exporting Wnt proteins. Development 2023; 150:286996. [PMID: 36763105 PMCID: PMC10112924 DOI: 10.1242/dev.201352] [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: 02/11/2023]
Abstract
Intercellular communication by Wnt proteins governs many essential processes during development, tissue homeostasis and disease in all metazoans. Many context-dependent effects are initiated in the Wnt-producing cells and depend on the export of lipidated Wnt proteins. Although much focus has been on understanding intracellular Wnt signal transduction, the cellular machinery responsible for Wnt secretion became better understood only recently. After lipid modification by the acyl-transferase Porcupine, Wnt proteins bind their dedicated cargo protein Evi/Wntless for transport and secretion. Evi/Wntless and Porcupine are conserved transmembrane proteins, and their 3D structures were recently determined. In this Review, we summarise studies and structural data highlighting how Wnts are transported from the ER to the plasma membrane, and the role of SNX3-retromer during the recycling of its cargo receptor Evi/Wntless. We also describe the regulation of Wnt export through a post-translational mechanism and review the importance of Wnt secretion for organ development and cancer, and as a future biomarker.
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Affiliation(s)
- Lucie Wolf
- German Cancer Research Center (DKFZ), Division of Signalling and Functional Genomics and Heidelberg University, BioQuant and Department of Cell and Molecular Biology, 69120 Heidelberg, Germany
| | - Michael Boutros
- German Cancer Research Center (DKFZ), Division of Signalling and Functional Genomics and Heidelberg University, BioQuant and Department of Cell and Molecular Biology, 69120 Heidelberg, Germany
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Ma Y, Du C, Xie X, Zhang Y, Wang C, Xu J, Xia G, Yang Y. To explore the regulatory role of Wnt/P53/Caspase3 signal in mouse ovarian development based on LFQ proteomics. J Proteomics 2023; 272:104772. [PMID: 36414229 DOI: 10.1016/j.jprot.2022.104772] [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: 08/06/2022] [Revised: 10/31/2022] [Accepted: 11/08/2022] [Indexed: 11/21/2022]
Abstract
Early ovarian follicular development is regulated by multiple proteins and signaling pathways, including the Wnt gene. To explore the regulatory mechanism of Wnt signaling on early ovarian follicular development, ovaries from 17.5 days post coitum (17.5 dpc) mice were collected and cultured in vitro for four days in the presence of IWP2 as a Wnt activity inhibitor and KN93 as a CaMKII inhibitor. LFQ proteomics technique was then used to analyze the significant differentially abundant (P-SDA) 93 and 262 proteins in the IWP2 and KN93 groups, respectively. Of these, 63 up-regulated proteins and 30 down-regulated proteins were identified for IWP2, along with 3 significant KEGG pathways (P < 0.05). For the KN93 group, 168 up-regulated proteins and 94 down-regulated ones were P-SDA, with 9 significant KEGG pathways also noted (P < 0.05). In both IWP2 and KN93 groups, key pathways (Wnt signaling pathway, Notch signaling pathway, P53 signaling pathway, TGF-β signaling pathway, ovarian steroid production) and metabolic regulation (energy metabolism, metal ion metabolism) were found to be related to early ovarian follicular development. Finally, western blotting demonstrated the regulatory role of Wnt/P53/Caspase3 signaling pathway in mouse ovarian development. These results contribute new knowledge to the understanding of regulatory factors of early ovarian follicular development. SIGNIFICANCE: In this study, label-free quantification (LFQ) was used in combination with liquid chromatography-mass spectrometer (LC-MS/MS) to study potential changes in the proteomic profiles of embryonic mice subjected to Wnt inhibitor IWP2 and CaMKIIinhibitor KN93. In addition, bioinformatics and comparative analyses were performed using publicly available proteomics databases to further explore the underlying mechanisms associated with early mouse ovarian growth and development.
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Affiliation(s)
- Yabo Ma
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western, Ningxia University, Yinchuan, Ningxia 750021, China; School of Life Sciences, Ningxia University, Yinchuan, Ningxia 750021, China
| | - Changzheng Du
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western, Ningxia University, Yinchuan, Ningxia 750021, China; School of Life Sciences, Ningxia University, Yinchuan, Ningxia 750021, China
| | - Xianguo Xie
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western, Ningxia University, Yinchuan, Ningxia 750021, China; School of Life Sciences, Ningxia University, Yinchuan, Ningxia 750021, China
| | - Yan Zhang
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western, Ningxia University, Yinchuan, Ningxia 750021, China; School of Life Sciences, Ningxia University, Yinchuan, Ningxia 750021, China
| | - Chao Wang
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western, Ningxia University, Yinchuan, Ningxia 750021, China; School of Life Sciences, Ningxia University, Yinchuan, Ningxia 750021, China; State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jinrui Xu
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western, Ningxia University, Yinchuan, Ningxia 750021, China; School of Life Sciences, Ningxia University, Yinchuan, Ningxia 750021, China
| | - Guoliang Xia
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western, Ningxia University, Yinchuan, Ningxia 750021, China; School of Life Sciences, Ningxia University, Yinchuan, Ningxia 750021, China; State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yi Yang
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western, Ningxia University, Yinchuan, Ningxia 750021, China; School of Life Sciences, Ningxia University, Yinchuan, Ningxia 750021, China.
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Hsu SH, Chuang KT, Wang LT. Role of wnt ligand secretion mediator signaling in cancer development. JOURNAL OF CANCER RESEARCH AND PRACTICE 2023. [DOI: 10.4103/ejcrp.ejcrp-d-22-00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
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Molecular Genomic Study of Inhibin Molecule Production through Granulosa Cell Gene Expression in Inhibin-Deficient Mice. Molecules 2022; 27:molecules27175595. [PMID: 36080362 PMCID: PMC9458043 DOI: 10.3390/molecules27175595] [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: 08/11/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022] Open
Abstract
Inhibin is a molecule that belongs to peptide hormones and is excreted through pituitary gonadotropins stimulation action on the granulosa cells of the ovaries. However, the differential regulation of inhibin and follicle-stimulating hormone (FSH) on granulosa cell tumor growth in mice inhibin-deficient females is not yet well understood. The objective of this study was to evaluate the role of inhibin and FSH on the granulosa cells of ovarian follicles at the premature antral stage. This study stimulated immature wild-type (WT) and Inhibin-α knockout (Inha−/−) female mice with human chorionic gonadotropin (hCG) and examined hCG-induced gene expression changes in granulosa cells. Also, screening of differentially expressed genes (DEGs) was performed in the two groups under study. In addition, related modules to external traits and key gene drivers were determined through Weighted Gene Co-Expression Network Analysis (WGCNA) algorithm. The results identified a number of 1074 and 931 DEGs and 343 overlapping DEGs (ODEGs) were shared in the two groups. Some 341 ODEGs had high relevance and consistent expression direction, with a significant correlation coefficient (r2 = 0.9145). Additionally, the gene co-expression network of selected 153 genes showed 122 nodes enriched to 21 GO biological processes (BP) and reproduction and 3 genes related to genomic pathways. By using principal component analysis (PCA), the 14 genes in the regulatory network were fixed and the cumulative proportion of fitted top three principal components was 94.64%. In conclusion, this study revealed the novelty of using ODEGs for investigating the inhibin and FSH hormone pathways that might open the way toward gene therapy for granulosa cell tumors. Also, these genes could be used as biomarkers for tracking the changes in inhibin and FSH hormone from the changes in the nutrition pattern.
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