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Chen Q, Wu B, Li C, Ding L, Huang S, Wang J, Zhao J. Deciphering male influence in gynogenetic Pengze crucian carp ( Carassius auratus var. pengsenensis): insights from Nanopore sequencing of structural variations. Front Genet 2024; 15:1392110. [PMID: 38784042 PMCID: PMC11111978 DOI: 10.3389/fgene.2024.1392110] [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: 02/27/2024] [Accepted: 04/11/2024] [Indexed: 05/25/2024] Open
Abstract
In this study, we investigate gynogenetic reproduction in Pengze Crucian Carp (Carassius auratus var. pengsenensis) using third-generation Nanopore sequencing to uncover structural variations (SVs) in offspring. Our objective was to understand the role of male genetic material in gynogenesis by examining the genomes of both parents and their offspring. We discovered a notable number of male-specific structural variations (MSSVs): 1,195 to 1,709 MSSVs in homologous offspring, accounting for approximately 0.52%-0.60% of their detected SVs, and 236 to 350 MSSVs in heterologous offspring, making up about 0.10%-0.13%. These results highlight the significant influence of male genetic material on the genetic composition of offspring, particularly in homologous pairs, challenging the traditional view of asexual reproduction. The gene annotation of MSSVs revealed their presence in critical gene regions, indicating potential functional impacts. Specifically, we found 5 MSSVs in the exonic regions of protein-coding genes in homologous offspring, suggesting possible direct effects on protein structure and function. Validation of an MSSV in the exonic region of the polyunsaturated fatty acid 5-lipoxygenase gene confirmed male genetic material transmission in some offspring. This study underscores the importance of further research on the genetic diversity and gynogenesis mechanisms, providing valuable insights for reproductive biology, aquaculture, and fostering innovation in biological research and aquaculture practices.
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Affiliation(s)
- Qianhui Chen
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Biyu Wu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Chao Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Liyun Ding
- Jiangxi Fisheries Research Institute, Nanchang, China
| | - Shiting Huang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Junjie Wang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jun Zhao
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
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Zhang Y, Li D, Liu Y, Peng L, Lu D, Wang P, Ke D, Yang H, Zhu X, Ruan C. 3D-bioprinted anisotropic bicellular living hydrogels boost osteochondral regeneration via reconstruction of cartilage-bone interface. Innovation (N Y) 2024; 5:100542. [PMID: 38144040 PMCID: PMC10746383 DOI: 10.1016/j.xinn.2023.100542] [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: 07/27/2023] [Accepted: 11/17/2023] [Indexed: 12/26/2023] Open
Abstract
Reconstruction of osteochondral (OC) defects represents an immense challenge due to the need for synchronous regeneration of special stratified tissues. The revolutionary innovation of bioprinting provides a robust method for precise fabrication of tissue-engineered OCs with hierarchical structure; however, their spatial living cues for simultaneous fulfilment of osteogenesis and chondrogenesis to reconstruct the cartilage-bone interface of OC are underappreciated. Here, inspired by natural OC bilayer features, anisotropic bicellular living hydrogels (ABLHs) simultaneously embedding articular cartilage progenitor cells (ACPCs) and bone mesenchymal stem cells (BMSCs) in stratified layers were precisely fabricated via two-channel extrusion bioprinting. The optimum formulation of the 7% GelMA/3% AlgMA hydrogel bioink was demonstrated, with excellent printability at room temperature and maintained high cell viability. Moreover, the chondrogenic ability of ACPCs and the osteogenic ability of BMSCs were demonstrated in vitro, confirming the inherent differential spatial regulation of ABLHs. In addition, ABLHs exhibited satisfactory synchronous regeneration of cartilage and subchondral bone in vivo. Compared with homogeneous hydrogels, the neo-cartilage and neo-bone in ABLHs were augmented by 23.5% and 20.8%, respectively, and more important, a more harmonious cartilage-bone interface was achieved by ABLHs due to their well-tuned cartilage-bone-vessel crosstalk. We anticipate that such a strategy of tissue-mimetic ABLH by means of bioprinting is capable of spatiotemporal cell-driven regeneration, offering insights into the fabrication of anisotropic living materials for the reconstruction of complex organ defects.
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Affiliation(s)
- Yijian Zhang
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China
| | - Duo Li
- Research Center for Human Tissue and Organ Degeneration, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Liu
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China
| | - Liuqi Peng
- Research Center for Human Tissue and Organ Degeneration, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Dongdong Lu
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China
| | - Pinpin Wang
- Research Center for Human Tissue and Organ Degeneration, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Dongxu Ke
- Novaprint Therapeutics Suzhou Co., Ltd., Room 605, B1 Building, BioBay, No.218 Xinghu Street, Suzhou Industrial Park, Suzhou 215000, China
| | - Huilin Yang
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China
| | - Xuesong Zhu
- Department of Orthopaedics, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou 215006, China
| | - Changshun Ruan
- Research Center for Human Tissue and Organ Degeneration, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Qi H, Deng Z, Ye F, Gou J, Huang M, Xiang H, Li H. Analysis of the differentially expressed genes in the combs and testes of Qingyuan partridge roosters at different developmental stages. BMC Genomics 2024; 25:33. [PMID: 38177997 PMCID: PMC10768254 DOI: 10.1186/s12864-024-09960-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/01/2024] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND The sexual maturity of chickens is an important economic trait, and the breeding of precocious and delayed puberty roosters is an important selection strategy for broilers. The comb serves as an important secondary sexual characteristic of roosters and determines their sexual precocity. Moreover, comb development is closely associated with gonad development in roosters. However, the underlying molecular mechanism regulating the sexual maturity of roosters has not yet been fully explored. RESULTS In order to identify the genes related to precocious puberty in Qingyuan partridge roosters, and based on the synchrony of testis and combs development, combined with histological observation and RNA-seq method, the developmental status and gene expression profile of combs and testis were obtained. The results showed that during the early growth and development period (77 days of age), the development of combs and testis was significant in the high comb (H) group versus the low comb (L) group (p < 0.05); however, the morphological characteristic of the comb and testicular tissues converged during the late growth and development period (112 days of age) in the H and L groups. Based on these results, RNA-sequencing analysis was performed on the comb and testis tissues of the 77 and 112 days old Qingyuan Partridge roosters with different comb height traits. GO and KEGG analysis enrichment analysis showed that the differentially expressed genes were primarily enriched in MAPK signaling, VEGF signaling, and retinol metabolism pathways. Moreover, weighted correlation network analysis and module co-expression network analysis identified WNT6, AMH, IHH, STT3A, PEX16, KPNA7, CATHL2, ROR2, PAMR1, WISP2, IL17REL, NDRG4, CYP26B1, and CRHBP as the key genes associated with the regulation of precocity and delayed puberty in Qingyuan Partridge roosters. CONCLUSIONS In summary, we identified the key regulatory genes of sexual precocity in roosters, which provide a theoretical basis for understanding the developmental differences between precocious and delayed puberty in roosters.
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Affiliation(s)
- Hao Qi
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, 528225, Foshan, Guangdong, China
| | - Zhidan Deng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, 528225, Foshan, Guangdong, China
| | - Fei Ye
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, 528225, Foshan, Guangdong, China
| | - Junwei Gou
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, 528225, Foshan, Guangdong, China
| | - Miaoxin Huang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, 528225, Foshan, Guangdong, China
| | - Hai Xiang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, 528225, Foshan, Guangdong, China
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, 528225, Foshan, Guangdong, China.
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Reyes-Pérez P, García-Marín LM, Aman AM, Antar T, Flores-Ocampo V, Mitchell BL, Medina-Rivera A, Rentería ME. Investigating the Shared Genetic Etiology Between Parkinson's Disease and Depression. JOURNAL OF PARKINSON'S DISEASE 2024; 14:483-493. [PMID: 38457145 DOI: 10.3233/jpd-230176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Background Depression is a common symptom in Parkinson's disease (PD), resulting from underlying neuropathological processes and psychological factors. However, the extent to which shared genetic risk factors contribute to the relationship between depression and PD is poorly understood. Objective To examine the effects of common genetic variants influencing the etiology of PD and depression risk at the genome-wide and local genomic regional level. Methods We comprehensively investigated the genetic relationship between PD and depression using genome-wide association studies data. First, we estimated the genetic correlation at the genome-wide level using linkage-disequilibrium score regression, followed by local genetic correlation analysis using the GWAS-pairwise method and functional annotation to identify genes that may jointly influence the risk for both traits. Also, we performed Latent Causal Variable, Latent Heritable Confounder Mendelian Randomization, and traditional Mendelian Randomization analyses to investigate the potential causal relationship. Results Although the genetic correlation between PD and depression was not statistically significant at the genome-wide level, GWAS-pairwise analyses identified 16 genomic segments associated with PD and depression, implicating nine genes. Further analyses revealed distinct patterns within individual genes, suggesting an intricate pattern. These genes involve various biological processes, including neurotransmitter regulation, senescence, and nucleo-cytoplasmic transport mechanisms. We did not observe genetic evidence of causality between PD and depression. Conclusions Our findings did not support a genome-wide genetic correlation or a causal association between both conditions. However, we identified genomic segments but identified genomic segments linked to distinct biological pathways influencing their etiology.Further research is needed to understand their functional consequences.
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Affiliation(s)
- Paula Reyes-Pérez
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Luis M García-Marín
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Asma M Aman
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Tarek Antar
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Victor Flores-Ocampo
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
- Licenciatura en Ciencias Genómicas, Escuela Nacional de Estudios Superiores Unidad Juriquilla, Universidad Nacional Autónoma de México, Querétaro, México
| | - Brittany L Mitchell
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Alejandra Medina-Rivera
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Miguel E Rentería
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD,Australia
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Bourne LE, Hesketh A, Sharma A, Bucca G, Bush PG, Staines KA. The effects of physiological and injurious hydrostatic pressure on murine ex vivo articular and growth plate cartilage explants: an RNAseq study. Front Endocrinol (Lausanne) 2023; 14:1278596. [PMID: 38144567 PMCID: PMC10740163 DOI: 10.3389/fendo.2023.1278596] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
Introduction Chondrocytes are continuously exposed to loads placed upon them. Physiological loads are pivotal to the maintenance of articular cartilage health, while abnormal loads contribute to pathological joint degradation. Similarly, the growth plate cartilage is subject to various loads during growth and development. Due to the high-water content of cartilage, hydrostatic pressure is considered one of the main biomechanical influencers on chondrocytes and has been shown to play an important role in the mechano-regulation of cartilage. Methods Herein, we conducted RNAseq analysis of ex vivo hip cap (articular), and metatarsal (growth plate) cartilage cultures subjected to physiological (5 MPa) and injurious (50 MPa) hydrostatic pressure, using the Illumina platform (n = 4 replicates). Results Several hundreds of genes were shown to be differentially modulated by hydrostatic pressure, with the majority of these changes evidenced in hip cap cartilage cultures (375 significantly upregulated and 322 downregulated in 5 MPa versus control; 1022 upregulated and 724 downregulated in 50 MPa versus control). Conversely, fewer genes were differentially affected by hydrostatic pressure in the metatarsal cultures (5 significantly upregulated and 23 downregulated in 5 MPa versus control; 7 significantly upregulated and 19 downregulated in 50 MPa versus control). Using Gene Ontology annotations for Biological Processes, in the hip cap data we identified a number of pathways that were modulated by both physiological and injurious hydrostatic pressure. Pathways upregulated in response to 50 MPa versus control, included those involved in the generation of precursor metabolites and cellular respiration. Biological processes that were downregulated in this tissue included ossification, connective tissue development, and chondrocyte differentiation. Discussion Collectively our data highlights the divergent chondrocyte phenotypes in articular and growth plate cartilage. Further, we show that the magnitude of hydrostatic pressure application has distinct effects on gene expression and biological processes in hip cap cartilage explants. Finally, we identified differential expression of a number of genes that have previously been identified as osteoarthritis risk genes, including Ctsk, and Chadl. Together these data may provide potential genetic targets for future investigations in osteoarthritis research and novel therapeutics.
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Affiliation(s)
- Lucie E. Bourne
- Centre for Lifelong Health, School of Applied Sciences, University of Brighton, Brighton, United Kingdom
| | - Andrew Hesketh
- Centre for Lifelong Health, School of Applied Sciences, University of Brighton, Brighton, United Kingdom
| | - Aikta Sharma
- Department of Mechanical Engineering, University College London, London, United Kingdom
| | - Giselda Bucca
- Centre for Lifelong Health, School of Applied Sciences, University of Brighton, Brighton, United Kingdom
| | - Peter G. Bush
- Centre for Lifelong Health, School of Applied Sciences, University of Brighton, Brighton, United Kingdom
| | - Katherine A. Staines
- Centre for Lifelong Health, School of Applied Sciences, University of Brighton, Brighton, United Kingdom
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Bharati J, Kumar S, Mohan NH, Chandra Das B, Devi SJ, Gupta VK. Ovarian follicle transcriptome dynamics reveals enrichment of immune system process during transition from small to large follicles in cyclic Indian Ghoongroo pigs. J Reprod Immunol 2023; 160:104164. [PMID: 37924675 DOI: 10.1016/j.jri.2023.104164] [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: 05/10/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 11/06/2023]
Abstract
Ovarian follicular development is a critical determinant of reproductive performance in litter bearing species like pigs, wherein economic gains depend on litter size. The study aimed to gain insight into the differentially expressed genes (DEGs) and signalling pathways regulating follicular growth and maturation in Ghoongroo pigs. Transcriptome profiling of porcine small follicles (SF) and large follicles (LF) was conducted using NovaSeq600 sequencing platform and DEGs were identified using DESeq2 with threshold of Padj. < 0.05 and log2 fold change cut off 0.58 (LF vs. SF). Functional annotations and bioinformatics analysis of DEGs were performed to find out biological functions, signalling pathways and hub genes regulating follicular dynamics. Transcriptome analysis revealed 709 and 479 genes unique to SF and LF stages, respectively, and 11,993 co-expressed genes in both the groups. In total, 507 DEGs (284 upregulated and 223 downregulated) were identified, which encoded for diverse proteins including transcription factors (TFs). These DEGs were functionally linked to response to stimulus, lipid metabolic process, developmental process, extracellular matrix organisation along with the immune system process, indicating wide-ranging mechanisms associated with follicular transition. The enriched KEGG pathways in LF stage consisted of ovarian steroidogenesis, cholesterol and retinol metabolism, cell adhesion molecules, cytokine receptor interaction and immune signalling pathways, depicting intra-follicular control of varied ovarian function. The hub gene analysis revealed APOE, SCARB1, MMP9, CYP17A1, TYROBP as key regulators of follicular development. This study identified candidate genes and TFs providing steroidogenic advantage to LFs which makes them fit for selection into the ovulatory pool of follicles.
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Affiliation(s)
- Jaya Bharati
- Animal Physiology, ICAR-National Research Centre on Pig, Rani, 781131 Guwahati, Assam, India.
| | - Satish Kumar
- Animal Genetics and Breeding, ICAR-National Research Centre on Pig, Rani, 781131 Guwahati, Assam, India
| | - N H Mohan
- Animal Physiology, ICAR-National Research Centre on Pig, Rani, 781131 Guwahati, Assam, India
| | - Bikash Chandra Das
- Animal Physiology, ICAR-National Research Centre on Pig, Rani, 781131 Guwahati, Assam, India
| | - Salam Jayachitra Devi
- Computer Applications and Information Technology, ICAR-National Research Centre on Pig, Rani, 781131 Guwahati, Assam, India
| | - Vivek Kumar Gupta
- Director, ICAR-National Research Centre on Pig, Rani, 781131 Guwahati, Assam, India
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Maiti G, Ashworth S, Choi T, Chakravarti S. Molecular cues for immune cells from small leucine-rich repeat proteoglycans in their extracellular matrix-associated and free forms. Matrix Biol 2023; 123:48-58. [PMID: 37793508 PMCID: PMC10841460 DOI: 10.1016/j.matbio.2023.10.001] [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: 06/01/2023] [Revised: 09/14/2023] [Accepted: 10/01/2023] [Indexed: 10/06/2023]
Abstract
In this review we highlight emerging immune regulatory functions of lumican, keratocan, fibromodulin, biglycan and decorin, which are members of the small leucine-rich proteoglycans (SLRP) of the extracellular matrix (ECM). These SLRPs have been studied extensively as collagen-fibril regulatory structural components of the skin, cornea, bone and cartilage in homeostasis. However, SLRPs released from a remodeling ECM, or synthesized by activated fibroblasts and immune cells contribute to an ECM-free pool in tissues and circulation, that may have a significant, but poorly understood foot print in inflammation and disease. Their molecular interactions and the signaling networks they influence also require investigations. Here we present studies on the leucine-rich repeat (LRR) motifs of SLRP core proteins, their evolutionary and functional relationships with other LRR pathogen recognition receptors, such as the toll-like receptors (TLRs) to bring some molecular clarity in the immune regulatory functions of SLRPs. We discuss molecular interactions of fragments and intact SLRPs, and how some of these interactions are likely modulated by glycosaminoglycan side chains. We integrate findings on molecular interactions of these SLRPs together with what is known about their presence in circulation and lymph nodes (LN), which are important sites of immune cell regulation. Recent bulk and single cell RNA sequencing studies have identified subsets of stromal reticular cells that express these SLRPs within LNs. An understanding of the cellular source, molecular interactions and signaling consequences will lead to a fundamental understanding of how SLRPs modulate immune responses, and to therapeutic tools based on these SLRPs in the future.
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Affiliation(s)
- George Maiti
- Department of Ophthalmology, NYU Grossman School of Medicine, New York, NY, United States
| | - Sean Ashworth
- Department of Ophthalmology, NYU Grossman School of Medicine, New York, NY, United States
| | - Tansol Choi
- Department of Ophthalmology, NYU Grossman School of Medicine, New York, NY, United States
| | - Shukti Chakravarti
- Department of Ophthalmology, NYU Grossman School of Medicine, New York, NY, United States; Department of Pathology, NYU Grossman School of Medicine, New York, NY, United States.
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McCabe MC, Okamura DM, Erickson CB, Perry BW, Brewer CM, Nguyen ED, Saviola AJ, Majesky MW, Hansen KC. ECM-Focused Proteomic Analysis of Ear Punch Regeneration in Acomys Cahirinus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.11.561940. [PMID: 37873317 PMCID: PMC10592745 DOI: 10.1101/2023.10.11.561940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
In mammals, significant injury is generally followed by the formation of a fibrotic scar which provides structural integrity but fails to functionally restore damaged tissue. Spiny mice of the genus Acomys represent the first example of full skin autotomy in mammals. Acomys cahirinus has evolved extremely weak skin as a strategy to avoid predation and is able to repeatedly regenerate healthy tissue without scar after severe skin injury or full-thickness ear punches. Extracellular matrix (ECM) composition is a critical regulator of wound repair and scar formation and previous studies have suggested that alterations in its expression may be responsible for the differences in regenerative capacity observed between Mus musculus and A. cahirinus , yet analysis of this critical tissue component has been limited in previous studies by its insolubility and resistance to extraction. Here, we utilize a 2-step ECM-optimized extraction to perform proteomic analysis of tissue composition during wound repair after full-thickness ear punches in A. cahirinus and M. musculus from weeks 1 to 4 post-injury. We observe changes in a wide range of ECM proteins which have been previously implicated in wound regeneration and scar formation, including collagens, coagulation and provisional matrix proteins, and matricryptic signaling peptides. We additionally report differences in crosslinking enzyme activity and ECM protein solubility between Mus and Acomys. Furthermore, we observed rapid and sustained increases in CD206, a marker of pro-regenerative M2 macrophages, in Acomys, whereas little or no increase in CD206 was detected in Mus. Together, these findings contribute to a comprehensive understanding of tissue cues which drive the regenerative capacity of Acomys and identify a number of potential targets for future pro-regenerative therapies.
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Richard D, Capellini TD, Diekman BO. Epigenetics as a mediator of genetic risk in osteoarthritis: role during development, homeostasis, aging, and disease progression. Am J Physiol Cell Physiol 2023; 324:C1078-C1088. [PMID: 36971423 PMCID: PMC10191130 DOI: 10.1152/ajpcell.00574.2022] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023]
Abstract
The identification of genomic loci that are associated with osteoarthritis (OA) has provided a starting point for understanding how genetic variation activates catabolic processes in the joint. However, genetic variants can only alter gene expression and cellular function when the epigenetic environment is permissive to these effects. In this review, we provide examples of how epigenetic shifts at distinct life stages can alter the risk for OA, which we posit is critical for the proper interpretation of genome-wide association studies (GWAS). During development, intensive work on the growth and differentiation factor 5 (GDF5) locus has revealed the importance of tissue-specific enhancer activity in controlling both joint development and the subsequent risk for OA. During homeostasis in adults, underlying genetic risk factors may help establish beneficial or catabolic "set points" that dictate tissue function, with a strong cumulative effect on OA risk. During aging, methylation changes and the reorganization of chromatin can "unmask" the effects of genetic variants. The destructive function of variants that alter aging would only mediate effects after reproductive competence and thus avoid any evolutionary selection pressure, as consistent with larger frameworks of biological aging and its relationship to disease. A similar "unmasking" may occur during OA progression, which is supported by the finding of distinct expression quantitative trait loci (eQTLs) in chondrocytes depending on the degree of tissue degradation. Finally, we propose that massively parallel reporter assays (MPRAs) will be a valuable tool to test the function of putative OA GWAS variants in chondrocytes from different life stages.
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Affiliation(s)
- Daniel Richard
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States
| | - Brian O Diekman
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, and North Carolina State University, Raleigh, North Carolina, United States
- Thurston Arthritis Research Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
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Li P, He L, Lan Y, Fang J, Fan Z, Li Y. Intrauterine Growth Restriction Induces Adulthood Chronic Metabolic Disorder in Cardiac and Skeletal Muscles. Front Nutr 2022; 9:929943. [PMID: 35938117 PMCID: PMC9354130 DOI: 10.3389/fnut.2022.929943] [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: 04/27/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
Objective Although population-based studies of intrauterine growth restriction (IUGR) demonstrated a series of postnatal complications, several studies identified that IUGR could definitely cause dysfunction of metabolism of cardiac and skeletal muscles in the perinatal period and early life. However, it is still unknown if such metabolic alternation would remain for long term or not, and whether normal protein diet administration postnatally would protect the IUGR offsprings from a “catch-up growth” and be able to reverse the premature metabolic remodeling. Materials and Methods We established an IUGR rat model with pregnant rats and a low-protein diet, and the developmental phenotypes had been carefully recorded. The cardiac and skeletal muscles had been collected to undergo RNA-seq. Results According to a series of comparisons of transcriptomes among various developmental processes, programmed metabolic dysfunction and chronic inflammation activity had been identified by transcriptome sequencing in IUGR offsprings, even such rats presented a normal developmental curve or body weight after normal postnatal diet feeding. Conclusion The data revealed that IUGR had a significant adverse impact on long-term cardiovascular function in rats, even they exhibit good nutritional status. So that, the fetal stage adverse events would encode the lifelong disease risk, which could hide in young age. This study remaindered that the research on long-term molecular changes is important, and only nutrition improvement would not totally reverse the damage of IUGR.
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Affiliation(s)
- Ping Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Pediatrics, West China Second University Hospital, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Lewei He
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yue Lan
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jie Fang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Pediatrics, West China Second University Hospital, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Jie Fang,
| | - Zhenxin Fan
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- *Correspondence: Zhenxin Fan,
| | - Yifei Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Pediatrics, West China Second University Hospital, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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11
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Merrild NG, Holzmann V, Ariosa-Morejon Y, Faull PA, Coleman J, Barrell WB, Young G, Fischer R, Kelly DJ, Addison O, Vincent TL, Grigoriadis AE, Gentleman E. Local depletion of proteoglycans mediates cartilage tissue repair in an ex vivo integration model. Acta Biomater 2022; 149:179-188. [PMID: 35779773 DOI: 10.1016/j.actbio.2022.06.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/25/2022] [Accepted: 06/17/2022] [Indexed: 11/28/2022]
Abstract
Successfully replacing damaged cartilage with tissue-engineered constructs requires integration with the host tissue and could benefit from leveraging the native tissue's intrinsic healing capacity; however, efforts are limited by a poor understanding of how cartilage repairs minor defects. Here, we investigated the conditions that foster natural cartilage tissue repair to identify strategies that might be exploited to enhance the integration of engineered/grafted cartilage with host tissue. We damaged porcine articular cartilage explants and using a combination of pulsed SILAC-based proteomics, ultrastructural imaging, and catabolic enzyme blocking strategies reveal that integration of damaged cartilage surfaces is not driven by neo-matrix synthesis, but rather local depletion of proteoglycans. ADAMTS4 expression and activity are upregulated in injured cartilage explants, but integration could be reduced by inhibiting metalloproteinase activity with TIMP3. These observations suggest that catabolic enzyme-mediated proteoglycan depletion likely allows existing collagen fibrils to undergo cross-linking, fibrillogenesis, or entanglement, driving integration. Catabolic enzymes are often considered pathophysiological markers of osteoarthritis. Our findings suggest that damage-induced upregulation of metalloproteinase activity may be a part of a healing response that tips towards tissue destruction under pathological conditions and in osteoarthritis, but could also be harnessed in tissue engineering strategies to mediate repair. STATEMENT OF SIGNIFICANCE: Cartilage tissue engineering strategies require graft integration with the surrounding tissue; however, how the native tissue repairs minor injuries is poorly understood. We applied pulsed SILAC-based proteomics, ultrastructural imaging, and catabolic enzyme blocking strategies to a porcine cartilage explant model and found that integration of damaged cartilage surfaces is driven by catabolic enzyme-mediated local depletion of proteoglycans. Although catabolic enzymes have been implicated in cartilage destruction in osteoarthritis, our findings suggest that damage-induced upregulation of metalloproteinase activity may be a part of a healing response that tips towards tissue destruction under pathological conditions. They also suggest that this natural cartilage tissue repair process could be harnessed in tissue engineering strategies to enhance the integration of engineered cartilage with host tissue.
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Affiliation(s)
- Nicholas Groth Merrild
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
| | - Viktoria Holzmann
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
| | - Yoanna Ariosa-Morejon
- Centre for OA Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, UK
| | - Peter A Faull
- College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA
| | - Jennifer Coleman
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
| | - William B Barrell
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
| | - Gloria Young
- Department of Materials, Imperial College London, London SW7 2AZ, UK
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Daniel J Kelly
- Trinity Centre for Biomedical Engineering, Trinity College Dublin, Dublin 2, Ireland
| | - Owen Addison
- Centre for Oral, Clinical and Translational Sciences, King's College London, London SE1 9RT, UK
| | - Tonia L Vincent
- Centre for OA Pathogenesis Versus Arthritis, Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, UK
| | | | - Eileen Gentleman
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK.
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12
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Goldoni I, Ibelli AMG, Fernandes LT, Peixoto JDO, Hul LM, Cantão ME, Gouveia JJDS, Ledur MC. Comprehensive Analyses of Bone and Cartilage Transcriptomes Evince Ion Transport, Inflammation and Cartilage Development-Related Genes Involved in Chickens’ Femoral Head Separation. Animals (Basel) 2022; 12:ani12060788. [PMID: 35327184 PMCID: PMC8944783 DOI: 10.3390/ani12060788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Femoral head necrosis (FHN) and other locomotor problems cause severe impacts on the poultry industry due to huge economic losses and reduced animal welfare. Femoral head separation (FHS), the initial phase of FHN, is usually a subclinical condition characterized by the detachment of articular cartilage from the bone. In this study, we aimed to identify genes and biological processes involved with FHS in broilers. A better understanding of the FHS molecular mechanisms can help to develop strategies to reduce this condition in chickens. Here, we described several genes that have their expression altered in the articular cartilage and femur when normal and FHS-affected animals were compared. Furthermore, genetic variants were found differing between the studied groups. Therefore, performing an integrated analysis of these datasets, we were able to detect genes and variants related to FHS in chickens. Some of them, such as SLC4A1, RHAG, ANK1, MKNK2, SPTB, ADA, C7 and EPB420 genes were highlighted and should be further explored to validate them as candidates to FHS and FHN in chickens and possibly in humans. Abstract Femoral head separation (FHS) is usually a subclinical condition characterized by the detachment of articular cartilage from the bone. In this study, a comprehensive analysis identifying shared and exclusive expression profiles, biological processes (BP) and variants related to FHS in the femoral articular cartilage and growth plate in chickens was performed through RNA sequencing analysis. Thirty-six differentially expressed (DE) genes were shared between femoral articular cartilage (AC) and growth plate (GP) tissues. Out of those, 23 genes were enriched in BP related to ion transport, translation factors and immune response. Seventy genes were DE exclusively in the AC and 288 in the GP. Among the BP of AC, the response against bacteria can be highlighted, and for the GP tissue, the processes related to chondrocyte differentiation and cartilage development stand out. When the chicken DE genes were compared to other datasets, eight genes (SLC4A1, RHAG, ANK1, MKNK2, SPTB, ADA, C7 and EPB420) were shared between chickens and humans. Furthermore, 89 variants, including missense in the SPATS2L, PRKAB1 and TRIM25 genes, were identified between groups. Therefore, those genes should be more explored to validate them as candidates to FHS/FHN in chickens and humans.
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Affiliation(s)
- Iara Goldoni
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, R. Salvatore Renna, 875, Guarapuava 85015-430, PR, Brazil; (I.G.); (J.d.O.P.); (L.M.H.)
| | - Adriana Mércia Guaratini Ibelli
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, R. Salvatore Renna, 875, Guarapuava 85015-430, PR, Brazil; (I.G.); (J.d.O.P.); (L.M.H.)
- Embrapa Suínos e Aves, Rodovia BR 153, km 110, Concórdia 89715-899, SC, Brazil; (L.T.F.); (M.E.C.)
- Correspondence: (A.M.G.I.); (M.C.L.); Tel.: +55-49-3441-3217 (A.M.G.I.); +55-49-3441-0411 (M.C.L.)
| | - Lana Teixeira Fernandes
- Embrapa Suínos e Aves, Rodovia BR 153, km 110, Concórdia 89715-899, SC, Brazil; (L.T.F.); (M.E.C.)
| | - Jane de Oliveira Peixoto
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, R. Salvatore Renna, 875, Guarapuava 85015-430, PR, Brazil; (I.G.); (J.d.O.P.); (L.M.H.)
- Embrapa Suínos e Aves, Rodovia BR 153, km 110, Concórdia 89715-899, SC, Brazil; (L.T.F.); (M.E.C.)
| | - Ludmila Mudri Hul
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, R. Salvatore Renna, 875, Guarapuava 85015-430, PR, Brazil; (I.G.); (J.d.O.P.); (L.M.H.)
| | - Maurício Egídio Cantão
- Embrapa Suínos e Aves, Rodovia BR 153, km 110, Concórdia 89715-899, SC, Brazil; (L.T.F.); (M.E.C.)
| | - João José de Simoni Gouveia
- Programa de Pós-Graduação em Ciências Veterinárias no Semiárido, Universidade Federal do Vale do São Francisco, UNIVASF, Rodovia BR 407, 12 Lote 543, Petrolina 56300-000, PE, Brazil;
| | - Mônica Corrêa Ledur
- Embrapa Suínos e Aves, Rodovia BR 153, km 110, Concórdia 89715-899, SC, Brazil; (L.T.F.); (M.E.C.)
- Programa de Pós-Graduação em Zootecnia, UDESC-Oeste, Rua Beloni Trombeta Zanin, 680E, Chapecó 89815-630, SC, Brazil
- Correspondence: (A.M.G.I.); (M.C.L.); Tel.: +55-49-3441-3217 (A.M.G.I.); +55-49-3441-0411 (M.C.L.)
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13
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Shengnan Q, Bennett S, Wen W, Aiguo L, Jiake X. The role of tendon derived stem/progenitor cells and extracellular matrix components in the bone tendon junction repair. Bone 2021; 153:116172. [PMID: 34506992 DOI: 10.1016/j.bone.2021.116172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/22/2021] [Accepted: 09/02/2021] [Indexed: 12/29/2022]
Abstract
Fibrocartilage enthesis is the junction between bone and tendon with a typical characteristics of fibrocartilage transition zones. The regeneration of this transition zone is the bottleneck for functional restoration of bone tendon junction (BTJ). Biomimetic approaches, especially decellularized extracellular matrix (ECM) materials, are strategies which aim to mimic the components of tissues to the utmost extent, and are becoming popular in BTJ healing because of their ability not only to provide scaffolds to allow cells to attach and migrate, but also to provide a microenvironment to guide stem/progenitor cells lineage-specific differentiation. However, the cellular and molecular mechanisms of those approaches, especially the ECM proteins, remain unclear. For BTJ reconstruction, fibrocartilage regeneration is the key for good integrity of bone and tendon as well as its mechanical recovery, so the components which can guide stem cells to a chondrogenic commitment in biomimetic approaches might well be the key for fibrocartilage regeneration and eventually for the better BTJ healing. In this review, we firstly discuss the importance of cartilage-like formation in the healing process of BTJ. Next, we explore the possibility of tendon-derived stem/progenitor cells as cell sources for BTJ regeneration due to their multi-differentiation potential. Finally, we summarize the role of extracellular matrix components of BTJ in guiding stem cell fate to a chondrogenic commitment, so as to provide cues for understanding the mechanisms of lineage-specific potential of biomimetic approaches as well as to inspire researchers to incorporate unique ECM components that facilitate BTJ repair into design.
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Affiliation(s)
- Qin Shengnan
- Guangzhou Institute of Traumatic Surgery, Department of Orthopedics, Guangzhou Red Cross Hospital, Medical College, Jinan University, Guangzhou, China
| | - Samuel Bennett
- School of Biomedical Sciences, The University of Western Australia, Perth, Australia
| | - Wang Wen
- Guangzhou Institute of Traumatic Surgery, Department of Orthopedics, Guangzhou Red Cross Hospital, Medical College, Jinan University, Guangzhou, China
| | - Li Aiguo
- Guangzhou Institute of Traumatic Surgery, Department of Orthopedics, Guangzhou Red Cross Hospital, Medical College, Jinan University, Guangzhou, China.
| | - Xu Jiake
- School of Biomedical Sciences, The University of Western Australia, Perth, Australia.
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14
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Yang C, Zhou Y, Marcus S, Formenti G, Bergeron LA, Song Z, Bi X, Bergman J, Rousselle MMC, Zhou C, Zhou L, Deng Y, Fang M, Xie D, Zhu Y, Tan S, Mountcastle J, Haase B, Balacco J, Wood J, Chow W, Rhie A, Pippel M, Fabiszak MM, Koren S, Fedrigo O, Freiwald WA, Howe K, Yang H, Phillippy AM, Schierup MH, Jarvis ED, Zhang G. Evolutionary and biomedical insights from a marmoset diploid genome assembly. Nature 2021; 594:227-233. [PMID: 33910227 PMCID: PMC8189906 DOI: 10.1038/s41586-021-03535-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 04/12/2021] [Indexed: 01/23/2023]
Abstract
The accurate and complete assembly of both haplotype sequences of a diploid organism is essential to understanding the role of variation in genome functions, phenotypes and diseases1. Here, using a trio-binning approach, we present a high-quality, diploid reference genome, with both haplotypes assembled independently at the chromosome level, for the common marmoset (Callithrix jacchus), an primate model system that is widely used in biomedical research2,3. The full spectrum of heterozygosity between the two haplotypes involves 1.36% of the genome-much higher than the 0.13% indicated by the standard estimation based on single-nucleotide heterozygosity alone. The de novo mutation rate is 0.43 × 10-8 per site per generation, and the paternal inherited genome acquired twice as many mutations as the maternal. Our diploid assembly enabled us to discover a recent expansion of the sex-differentiation region and unique evolutionary changes in the marmoset Y chromosome. In addition, we identified many genes with signatures of positive selection that might have contributed to the evolution of Callithrix biological features. Brain-related genes were highly conserved between marmosets and humans, although several genes experienced lineage-specific copy number variations or diversifying selection, with implications for the use of marmosets as a model system.
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Affiliation(s)
- Chentao Yang
- BGI-Shenzhen, Shenzhen, China.,Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Stephanie Marcus
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | - Giulio Formenti
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA.,Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Lucie A Bergeron
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zhenzhen Song
- University of the Chinese Academy of Sciences, Beijing, China
| | | | - Juraj Bergman
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | | | | | | | - Yuan Deng
- BGI-Shenzhen, Shenzhen, China.,Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Duo Xie
- BGI-Shenzhen, Shenzhen, China
| | | | | | | | - Bettina Haase
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Jennifer Balacco
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | | | | | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology, Dresden, Germany
| | | | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Winrich A Freiwald
- Laboratory of Neural Systems, The Rockefeller University, New York, NY, USA.,Center for Brains, Minds and Machines (CBMM), The Rockefeller University, New York, NY, USA
| | | | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,University of the Chinese Academy of Sciences, Beijing, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China.,Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen, China
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Erich D Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA.,Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Guojie Zhang
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark. .,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,China National GeneBank, BGI-Shenzhen, Shenzhen, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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15
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Liu Y, Tu Y, Zhang M, Zou J, Ji G, Shan Y, Ju X, Shu J. Study on CHADL as a candidate gene for comb growth traits in Partridge Shank roosters. CANADIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1139/cjas-2018-0243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The comb is an important secondary sexual characteristic and comb growth traits, such as size and color of the comb, are widely used as indicators in chicken breeding programs. However, the genetic basis for these traits remains mostly unknown. It was found that the chondroadherin-like (CHADL) gene was up-regulated in large combs and was located in reported comb growth quantitative trait loci. In this study, tissue-specific expressions, expression patterns in combs of different ages, and CHADL polymorphisms were analyzed to investigate the relationship between this gene and comb growth traits of Partridge Shank roosters. The results showed that CHADL was more highly expressed in combs than in 10 other tissues, and its expressions in combs tended to gradually increase from the 5-wk-old mark to the 26-wk-old mark. The single-nucleotide polymorphism rs316423539 in the CHADL gene was significantly associated with the comb area and height, whereas rs14822286 was highly correlated with the comb color. Moreover, H1H5, H1H6, and H3H6 were the most advantageous genotype combinations for comb growth traits. Our results might help understand the molecular mechanism of comb growth traits and improve these traits directly by marker assistant selections.
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Affiliation(s)
- Yifan Liu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Institute of Poultry Sciences, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu Province 225000, People’s Republic of China
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Institute of Poultry Sciences, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu Province 225000, People’s Republic of China
| | - Yunjie Tu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Institute of Poultry Sciences, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu Province 225000, People’s Republic of China
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Institute of Poultry Sciences, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu Province 225000, People’s Republic of China
| | - Ming Zhang
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Institute of Poultry Sciences, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu Province 225000, People’s Republic of China
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Institute of Poultry Sciences, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu Province 225000, People’s Republic of China
| | - Jianmin Zou
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Institute of Poultry Sciences, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu Province 225000, People’s Republic of China
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Institute of Poultry Sciences, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu Province 225000, People’s Republic of China
| | - Gaige Ji
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Institute of Poultry Sciences, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu Province 225000, People’s Republic of China
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Institute of Poultry Sciences, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu Province 225000, People’s Republic of China
| | - Yanju Shan
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Institute of Poultry Sciences, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu Province 225000, People’s Republic of China
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Institute of Poultry Sciences, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu Province 225000, People’s Republic of China
| | - Xiaojun Ju
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Institute of Poultry Sciences, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu Province 225000, People’s Republic of China
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Institute of Poultry Sciences, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu Province 225000, People’s Republic of China
| | - Jingting Shu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Institute of Poultry Sciences, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu Province 225000, People’s Republic of China
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Institute of Poultry Sciences, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu Province 225000, People’s Republic of China
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16
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Ocken AR, Ku MM, Kinzer-Ursem TL, Calve S. Perlecan Knockdown Significantly Alters Extracellular Matrix Composition and Organization During Cartilage Development. Mol Cell Proteomics 2020; 19:1220-1235. [PMID: 32381549 PMCID: PMC7338092 DOI: 10.1074/mcp.ra120.001998] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/05/2020] [Indexed: 02/05/2023] Open
Abstract
Perlecan is a critical proteoglycan found in the extracellular matrix (ECM) of cartilage. In healthy cartilage, perlecan regulates cartilage biomechanics and we previously demonstrated perlecan deficiency leads to reduced cellular and ECM stiffness in vivo This change in mechanics may lead to the early onset osteoarthritis seen in disorders resulting from perlecan knockdown such as Schwartz-Jampel syndrome (SJS). To identify how perlecan knockdown affects the material properties of developing cartilage, we used imaging and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to study the ECM in a murine model of SJS, Hspg2C1532Y-Neo Perlecan knockdown led to defective pericellular matrix formation, whereas the abundance of bulk ECM proteins, including many collagens, increased. Post-translational modifications and ultrastructure of collagens were not significantly different; however, LC-MS/MS analysis showed more protein was secreted by Hspg2C1532Y-Neo cartilage in vitro, suggesting that the incorporation of newly synthesized ECM was impaired. In addition, glycosaminoglycan deposition was atypical, which may explain the previously observed decrease in mechanics. Overall, these findings provide insight into the influence of perlecan on functional cartilage assembly and the progression of osteoarthritis in SJS.
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Affiliation(s)
- Alexander R Ocken
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana
| | - Madeline M Ku
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana
| | | | - Sarah Calve
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana.
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17
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RNA-seq reveals downregulated osteochondral genes potentially related to tibia bacterial chondronecrosis with osteomyelitis in broilers. BMC Genet 2020; 21:58. [PMID: 32493207 PMCID: PMC7271470 DOI: 10.1186/s12863-020-00862-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/18/2020] [Indexed: 12/14/2022] Open
Abstract
Background Bacterial chondronecrosis with osteomyelitis (BCO) develops in the growth plate (GP) of the proximal femur and tibia and is initiated by damage to the less mineralized chondrocytes followed by colonization of opportunistic bacteria. This condition affects approximately 1% of all birds housed, being considered one of the major causes of lameness in fast growing broilers. Although several studies have been previously performed aiming to understand its pathogenesis, the molecular mechanisms involved with BCO remains to be elucidated. Therefore, this study aimed to generate a profile of global differential gene expression involved with BCO in the tibia of commercial broilers, through RNA sequencing analysis to identity genes and molecular pathways involved with BCO in chickens. Results Our data showed 192 differentially expressed (DE) genes: 63 upregulated and 129 downregulated in the GP of the tibia proximal epiphysis of BCO-affected broilers. Using all DE genes, six Biological Processes (BP) were associated with bone development (connective tissue development, cartilage development, skeletal system development, organ morphogenesis, system development and skeletal system morphogenesis). The analyses of the upregulated genes did not indicate any significant BP (FDR < 0.05). However, with the downregulated genes, the same BP were identified when using all DE genes in the analysis, with a total of 26 coding genes explaining BCO in the tibia: ACAN, ALDH1A2, CDH7, CHAD, CHADL, COL11A1, COMP, CSGALNACT1, CYR61, FRZB, GAL3ST1, HAPLN1, IHH, KIF26B, LECT1, LPPR1, PDE6B, RBP4A, SERINC5, SFRP1, SOX8, SOX9, TENM2, THBS1, UCHL1 and WFIKKN2. In addition, seven transcription factors were also associated to BCO: NFATC2, MAFB, HIF1A-ARNT, EWSR1-FLI1, NFIC, TCF3 and NF-KAPPAB. Conclusions Our data show that osteochondral downregulated genes are potential molecular causes of BCO in broilers, and the bacterial process seems to be, in fact, a secondary condition. Sixteen genes responsible for bone and cartilage formation were downregulated in BCO-affected broilers being strong candidate genes to trigger this disorder.
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18
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Patil K, Yelamanchi S, Kumar M, Hinduja I, Prasad TSK, Gowda H, Mukherjee S. Quantitative mass spectrometric analysis to unravel glycoproteomic signature of follicular fluid in women with polycystic ovary syndrome. PLoS One 2019; 14:e0214742. [PMID: 30946770 PMCID: PMC6448921 DOI: 10.1371/journal.pone.0214742] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 03/19/2019] [Indexed: 12/23/2022] Open
Abstract
Polycystic ovary syndrome (PCOS) is a complex endocrinopathy affecting women of reproductive age, and whose etiology is not well understood yet. In these women, the follicular growth is arrested at preantral stage leading to cyst formation, consequently resulting in anovulatory infertility in these women. As the follicular fluid provides the conducive microenvironment for the growth of oocytes, molecular profiling of the fluid may provide unique information about pathophysiology associated with follicular development in PCOS. Post-translational addition of oligosaccharide residues is one of the many modifications of secreted proteins influencing their functions. These glycoproteins play a significant role in disease pathology. Despite glycoproteins having such essential functions, very limited information is available on their profiling in human reproductive system, and glycoproteomic profile of follicular fluid of women with PCOS is yet unexplored. In the present study, we performed a comparative glycoproteomic analysis of follicular fluid between women with PCOS and controls undergoing in vitro fertilization, by enrichment of glycoproteins using three different lectins viz. concanavalin A, wheat germ agglutinin and Jacalin. Peptides generated by trypsin digestion were labeled with isobaric tags for relative and absolute quantification reagents and analyzed by liquid chromatography tandem mass spectrometry. We identified 10 differentially expressed glycoproteins, in the follicular fluid of women with PCOS compared to controls. Two important differentially expressed proteins- SERPINA1 and ITIH4, were consistently upregulated and downregulated respectively, upon validation by immunoblotting in follicular fluid and real-time polymerase chain reaction in granulosa cells. These proteins play a role in angiogenesis and extracellular matrix stabilization, vital for follicle maturation. In conclusion, a comparative glycoproteomic profiling of follicular fluid from women with PCOS and controls revealed an altered expression of proteins which may contribute to the defects in follicle development in PCOS pathophysiology.
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Affiliation(s)
- Krutika Patil
- Department of Molecular Endocrinology, National Institute for Research in Reproductive Health, Indian Council of Medical Research, Mumbai, India
| | - Soujanya Yelamanchi
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Manish Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Indira Hinduja
- P.D. Hinduja National Hospital and Medical Research Centre, Mumbai, India
| | - T. S. Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Srabani Mukherjee
- Department of Molecular Endocrinology, National Institute for Research in Reproductive Health, Indian Council of Medical Research, Mumbai, India
- * E-mail:
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Cibrián Uhalte E, Wilkinson JM, Southam L, Zeggini E. Pathways to understanding the genomic aetiology of osteoarthritis. Hum Mol Genet 2018; 26:R193-R201. [PMID: 28977450 PMCID: PMC5886472 DOI: 10.1093/hmg/ddx302] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 07/25/2017] [Indexed: 02/07/2023] Open
Abstract
Osteoarthritis is a common, complex disease with no curative therapy. In this review, we summarize current knowledge on disease aetiopathogenesis and outline genetics and genomics approaches that are helping catalyse a much-needed improved understanding of the biological underpinning of disease development and progression.
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Affiliation(s)
- Elena Cibrián Uhalte
- Human Genetics and Cellular Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Jeremy Mark Wilkinson
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK
| | - Lorraine Southam
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.,Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
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Identification of molecular pathways and candidate genes associated with cocks' comb size trait by genome-wide transcriptome analysis. Sci Rep 2018; 8:2015. [PMID: 29386544 PMCID: PMC5792444 DOI: 10.1038/s41598-018-20373-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/16/2018] [Indexed: 11/08/2022] Open
Abstract
The comb of the male is an important secondary sexual characteristic. Although quantitative trait loci (QTLs) related to comb size have been identified, molecular mechanisms underlying this trait remain mostly unknown. In this study, RNA sequencing (RNA-seq) was employed to compare whole transcriptomic differences between two groups of Partridge Shank chickens that are divergent in comb sizes. A total of 563 differentially expressed genes (DEGs) were identified, including 277 up-regulated and 286 down-regulated DEGs. According to the animal QTL database, eight DEGs including BMP2 and CHADL matching the reported QTLs were associated with the comb size. Functional annotation analysis revealed that DEGs were involved in cell communication and calcium signaling. Protein-protein interaction network analysis showed that STK32A, PIK3R1, EDN1, HSPA5, and HSPA8 have an impact on comb growth. Moreover, potential alternative splicing events and single nucleotide polymorphisms were also identified. Our data provide a source for identifying genes and pathways with functions critical to comb size and accelerate studies involving molecular mechanisms of this sexual ornament.
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Whole-genome sequencing identifies rare genotypes in COMP and CHADL associated with high risk of hip osteoarthritis. Nat Genet 2017; 49:801-805. [DOI: 10.1038/ng.3816] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/23/2017] [Indexed: 12/13/2022]
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Ji Y, Rong X, Ye H, Zhang K, Lu Y. Proteomic analysis of aqueous humor proteins associated with cataract development. Clin Biochem 2015; 48:1304-9. [DOI: 10.1016/j.clinbiochem.2015.08.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 12/26/2022]
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24
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Negri G, Magini P, Milani D, Colapietro P, Rusconi D, Scarano E, Bonati MT, Priolo M, Crippa M, Mazzanti L, Wischmeijer A, Tamburrino F, Pippucci T, Finelli P, Larizza L, Gervasini C. From Whole Gene Deletion to Point Mutations of EP300-Positive Rubinstein-Taybi Patients: New Insights into the Mutational Spectrum and Peculiar Clinical Hallmarks. Hum Mutat 2015; 37:175-83. [PMID: 26486927 DOI: 10.1002/humu.22922] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/12/2015] [Indexed: 12/16/2022]
Abstract
Rubinstein-Taybi syndrome (RSTS) is a rare congenital neurodevelopmental disorder characterized by growth deficiency, skeletal abnormalities, dysmorphic features, and intellectual disability. Causative mutations in CREBBP and EP300 genes have been identified in ∼55% and ∼8% of affected individuals. To date, only 28 EP300 alterations in 29 RSTS clinically described patients have been reported. EP300 analysis of 22 CREBBP-negative RSTS patients from our cohort led us to identify six novel mutations: a 376-kb deletion depleting EP300 gene; an exons 17-19 deletion (c.(3141+1_3142-1)_(3590+1_3591-1)del/p.(Ile1047Serfs*30)); two stop mutations, (c.3829A>T/p.(Lys1277*) and c.4585C>T/p.(Arg1529*)); a splicing mutation (c.1878-12A>G/p.(Ala627Glnfs*11)), and a duplication (c.4640dupA/p.(Asn1547Lysfs*3)). All EP300-mutated individuals show a mild RSTS phenotype and peculiar findings including maternal gestosis, skin manifestation, especially nevi or keloids, back malformations, and a behavior predisposing to anxiety. Furthermore, the patient carrying the complete EP300 deletion does not show a markedly severe clinical picture, even if a more composite phenotype was noticed. By characterizing six novel EP300-mutated patients, this study provides further insights into the EP300-specific clinical presentation and expands the mutational repertoire including the first case of a whole gene deletion. These new data will enhance EP300-mutated cases identification highlighting distinctive features and will improve the clinical practice allowing a better genotype-phenotype correlation.
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Affiliation(s)
- Gloria Negri
- Genetica Medica, Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italia
| | - Pamela Magini
- Laboratorio di Genetica Medica, Dipartimento di Scienze Mediche e Chirurgiche, Policlinico Ospedaliero Universitario S. Orsola-Malpighi, Bologna, Italia
| | - Donatella Milani
- Unità di Pediatria ad alta Intensità di Cura, Fondazione IRCCS Ca' Granda, Milano, Italia
| | - Patrizia Colapietro
- Genetica Medica, Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italia
| | - Daniela Rusconi
- Genetica Medica, Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italia
| | - Emanuela Scarano
- UO di Endocrinologia Pediatrica e Malattie Rare, Dipartimento di Pediatria, Ospedale Universitario S. Orsola Malpighi, Università degli Studi di Bologna, Bologna, Italia
| | - Maria Teresa Bonati
- Clinica di Genetica Medica, IRCCS Istituto Auxologico Italiano, Milano, Italia
| | - Manuela Priolo
- UOC Genetica Medica, Azienda Ospedaliera Bianchi-Melacrino-Morelli, Reggio Calabria, Italia
| | - Milena Crippa
- Laboratorio di Citogenetica e Genetica Molecolare, Centro di Ricerche e Tecnologie Biomediche, IRCCS Istituto Auxologico Italiano, Milano, Italia
| | - Laura Mazzanti
- UO di Endocrinologia Pediatrica e Malattie Rare, Dipartimento di Pediatria, Ospedale Universitario S. Orsola Malpighi, Università degli Studi di Bologna, Bologna, Italia
| | - Anita Wischmeijer
- Laboratorio di Genetica Medica, Dipartimento di Scienze Mediche e Chirurgiche, Policlinico Ospedaliero Universitario S. Orsola-Malpighi, Bologna, Italia
| | - Federica Tamburrino
- UO di Endocrinologia Pediatrica e Malattie Rare, Dipartimento di Pediatria, Ospedale Universitario S. Orsola Malpighi, Università degli Studi di Bologna, Bologna, Italia
| | - Tommaso Pippucci
- Laboratorio di Genetica Medica, Dipartimento di Scienze Mediche e Chirurgiche, Policlinico Ospedaliero Universitario S. Orsola-Malpighi, Bologna, Italia
| | - Palma Finelli
- Laboratorio di Citogenetica e Genetica Molecolare, Centro di Ricerche e Tecnologie Biomediche, IRCCS Istituto Auxologico Italiano, Milano, Italia.,Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milano, Italia
| | - Lidia Larizza
- Genetica Medica, Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italia.,Laboratorio di Citogenetica e Genetica Molecolare, Centro di Ricerche e Tecnologie Biomediche, IRCCS Istituto Auxologico Italiano, Milano, Italia
| | - Cristina Gervasini
- Genetica Medica, Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italia
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