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Salluzzo M, Vianello C, Flotta F, Rimondini R, Carboni L. MicroRNAs Associated with IgLON Cell Adhesion Molecule Expression. Curr Issues Mol Biol 2024; 46:7702-7718. [PMID: 39057097 PMCID: PMC11276434 DOI: 10.3390/cimb46070456] [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: 06/28/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
The IgLON family of cell adhesion molecules consists of five members (LSAMP, OPCML, neurotrimin, NEGR1, and IgLON5) discovered as supporters of neuronal development, axon growth and guidance, and synapse formation and maintenance. Tumour suppression properties have recently been emerging based on antiproliferative effects through the modulation of oncogenic pathways. Available evidence endorses a role for non-coding RNAs or microRNAs as relevant controllers of IgLON molecule expression that can impact their critical physiological and pathological roles. Current findings support a function for long non-coding RNAs and microRNAs in the modulation of LSAMP expression in cell senescence, cancer biogenesis, addiction, and pulmonary hypertension. For OPCML, data point to a role for several microRNAs in the control of tumorigenesis. MicroRNAs were detected in neurotrimin-mediated functions in cancer biogenesis and in Schwann cell responses to peripheral nerve injury. For NEGR1, studies have mainly investigated microRNA involvement in neuronal responses to ischaemic injury, although data also exist about tumorigenesis and endothelial cell dysfunction. For IgLON5, information is only available about microRNA involved in myocardial infarction. In conclusion, despite much information being still missing and further research needed, the emerging picture favours a model in which non-coding RNAs exert a crucial role in modulating IgLON expression, ultimately affecting their important physiological functions.
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Affiliation(s)
- Marco Salluzzo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, 40126 Bologna, Italy;
| | - Clara Vianello
- Department for Life Quality Studies, Alma Mater Studiorum University of Bologna, 47921 Rimini, Italy;
| | - Francesca Flotta
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40126 Bologna, Italy; (F.F.); (R.R.)
| | - Roberto Rimondini
- Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, 40126 Bologna, Italy; (F.F.); (R.R.)
| | - Lucia Carboni
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, 40126 Bologna, Italy;
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Zhang Z, Tang X, Li D, Tong X, Min L, Chen W, Ju X, Xu B. The Identification of RPL4 as a Hub Gene Associated with Goat Litter Size via Weighted Gene Co-Expression Network Analysis. Animals (Basel) 2024; 14:1470. [PMID: 38791687 PMCID: PMC11117213 DOI: 10.3390/ani14101470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Reproduction in goats is a highly complex and dynamic process of life regulation, involving coordinated regulation from various aspects such as central nervous system regulation, reproductive system development, oocyte maturation, and fertilized egg development. In recent years, researchers have identified numerous genes associated with goat reproductive performance through high-throughput sequencing, single-cell sequencing, gene knockout, and other techniques. However, there is still an urgent need to explore marker genes related to goat reproductive performance. In this study, a single-cell RNA sequencing dataset of oocytes (GSE136005) was obtained from the Gene Expression Omnibus (GEO) database. Weighted Gene Co-expression Network Analysis (WGCNA) was utilized to identify modules highly correlated with goat litter size. Through gene function enrichment analysis, it was found that genes within the modules were mainly enriched in adhesive junctions, cell cycle, and other signaling pathways. Additionally, the top 30 hub genes with the highest connectivity in WGCNA were identified. Subsequently, using Protein-Protein Interaction (PPI) network analysis, the top 30 genes with the highest connectivity within the modules were identified. The intersection of hub genes, key genes in the PPI network, and differentially expressed genes (DEGs) led to the identification of the RPL4 gene as a key marker gene associated with reproductive capacity in goat oocytes. Overall, our study reveals that the RPL4 gene in oocytes holds promise as a biological marker for assessing goat litter size, deepening our understanding of the regulatory mechanisms underlying goat reproductive performance.
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Affiliation(s)
- Zhifei Zhang
- Key Laboratory of Animal Nutrition and Feed Science in South Chian, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China; (Z.Z.); (X.T.); (D.L.); (X.T.); (L.M.); (W.C.)
- Heyuan Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Heyuan 517500, China
| | - Xueying Tang
- Key Laboratory of Animal Nutrition and Feed Science in South Chian, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China; (Z.Z.); (X.T.); (D.L.); (X.T.); (L.M.); (W.C.)
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Dagang Li
- Key Laboratory of Animal Nutrition and Feed Science in South Chian, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China; (Z.Z.); (X.T.); (D.L.); (X.T.); (L.M.); (W.C.)
| | - Xiong Tong
- Key Laboratory of Animal Nutrition and Feed Science in South Chian, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China; (Z.Z.); (X.T.); (D.L.); (X.T.); (L.M.); (W.C.)
| | - Li Min
- Key Laboratory of Animal Nutrition and Feed Science in South Chian, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China; (Z.Z.); (X.T.); (D.L.); (X.T.); (L.M.); (W.C.)
| | - Weidong Chen
- Key Laboratory of Animal Nutrition and Feed Science in South Chian, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China; (Z.Z.); (X.T.); (D.L.); (X.T.); (L.M.); (W.C.)
- Heyuan Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Heyuan 517500, China
| | - Xianghong Ju
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Bin Xu
- Key Laboratory of Animal Nutrition and Feed Science in South Chian, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510642, China; (Z.Z.); (X.T.); (D.L.); (X.T.); (L.M.); (W.C.)
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Martinez-Monleon A, Gaarder J, Djos A, Kogner P, Fransson S. Identification of recurrent 3q13.31 chromosomal rearrangement indicates LSAMP as a tumor suppressor gene in neuroblastoma. Int J Oncol 2023; 62:27. [PMID: 36601748 PMCID: PMC9851131 DOI: 10.3892/ijo.2023.5475] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 11/04/2022] [Indexed: 01/04/2023] Open
Abstract
Neuroblastoma (NB) is a childhood malignancy of the sympathetic nervous system. NB is mainly driven by copy number alterations, such as MYCN amplification, large deletions of chromosome arm 11q and gain of chromosome arm 17q, which are all markers of high‑risk disease. Genes targeted by recurrent, smaller, focal alterations include CDKN2A/B, TERT, PTPRD and ATRX. Our previous study on relapsed NB detected recurrent structural alterations centered at limbic system‑associated membrane protein (LSAMP; HUGO Gene Nomenclature Committee: 6705; chromosomal location 3q13.31), which is a gene frequently reported to be deleted or downregulated in other types of cancer. Notably, in cancer, LSAMP has been shown to have tumor‑suppressing functions. The present study performed an expanded investigation using whole genome sequencing of tumors from 35 patients, mainly with high‑risk NB. Focal duplications or deletions targeting LSAMP were detected in six cases (17%), whereas single nucleotide polymorphism‑microarray analysis of 16 NB cell lines detected segmental alterations at 3q13.31 in seven out of the 16 NB cell lines (44%). Furthermore, low expression of LSAMP in NB tumors was significantly associated with poor overall and event‑free survival. In vitro, knockdown of LSAMP in NB cell lines increased cell proliferation, whereas overexpression decreased proliferation and viability. These findings supported a tumor suppressor role for LSAMP in NB. However, the higher incidence of LSAMP aberrations in cell lines and in relapsed NB tumors suggested that these alterations were a late event predominantly in advanced NB with a poor prognosis, indicating a role of LSAMP in tumor progression rather than in tumor initiation. In conclusion, the present study demonstrated recurrent genomic aberrations of chromosomal region 3q13.31 that targeted the LSAMP gene, which encodes a membrane protein involved in cell adhesion, central nervous system development and neurite outgrowth. The frequent aberrations affecting LSAMP, together with functional evidence, suggested an anti‑proliferative role of LSAMP in NB.
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Affiliation(s)
- Angela Martinez-Monleon
- Department of Laboratory Medicine, Sahlgrenska Academy at University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Jennie Gaarder
- Department of Laboratory Medicine, Sahlgrenska Academy at University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Anna Djos
- Department of Laboratory Medicine, Sahlgrenska Academy at University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Per Kogner
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Susanne Fransson
- Department of Laboratory Medicine, Sahlgrenska Academy at University of Gothenburg, SE-405 30 Gothenburg, Sweden,Correspondence to: Dr Susanne Fransson, Department of Laboratory Medicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 3B, SE-405 30 Gothenburg, Sweden, E-mail:
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Jagomäe T, Singh K, Philips MA, Jayaram M, Seppa K, Tekko T, Gilbert SF, Vasar E, Lilleväli K. Alternative Promoter Use Governs the Expression of IgLON Cell Adhesion Molecules in Histogenetic Fields of the Embryonic Mouse Brain. Int J Mol Sci 2021; 22:6955. [PMID: 34203377 PMCID: PMC8268470 DOI: 10.3390/ijms22136955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/19/2021] [Accepted: 06/23/2021] [Indexed: 01/17/2023] Open
Abstract
The members of the IgLON superfamily of cell adhesion molecules facilitate fundamental cellular communication during brain development, maintain functional brain circuitry, and are associated with several neuropsychiatric disorders such as depression, autism, schizophrenia, and intellectual disabilities. Usage of alternative promoter-specific 1a and 1b mRNA isoforms in Lsamp, Opcml, Ntm, and the single promoter of Negr1 in the mouse and human brain has been previously described. To determine the precise spatiotemporal expression dynamics of Lsamp, Opcml, Ntm isoforms, and Negr1, in the developing brain, we generated isoform-specific RNA probes and carried out in situ hybridization in the developing (embryonic, E10.5, E11.5, 13.5, 17; postnatal, P0) and adult mouse brains. We show that promoter-specific expression of IgLONs is established early during pallial development (at E10.5), where it remains throughout its differentiation through adulthood. In the diencephalon, midbrain, and hindbrain, strong expression patterns are initiated a few days later and begin fading after birth, being only faintly expressed during adulthood. Thus, the expression of specific IgLONs in the developing brain may provide the means for regionally specific functionality as well as for specific regional vulnerabilities. The current study will therefore improve the understanding of how IgLON genes are implicated in the development of neuropsychiatric disorders.
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Affiliation(s)
- Toomas Jagomäe
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; (T.J.); (M.-A.P.); (M.J.); (K.S.); (E.V.); (K.L.)
- Centre of Excellence in Genomics and Translational Medicine, University of Tartu, 50090 Tartu, Estonia
- Laboratory Animal Centre, Institute of Biomedicine and Translational Medicine, University of Tartu, 14B Ravila Street, 50411 Tartu, Estonia
| | - Katyayani Singh
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; (T.J.); (M.-A.P.); (M.J.); (K.S.); (E.V.); (K.L.)
- Centre of Excellence in Genomics and Translational Medicine, University of Tartu, 50090 Tartu, Estonia
| | - Mari-Anne Philips
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; (T.J.); (M.-A.P.); (M.J.); (K.S.); (E.V.); (K.L.)
- Centre of Excellence in Genomics and Translational Medicine, University of Tartu, 50090 Tartu, Estonia
| | - Mohan Jayaram
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; (T.J.); (M.-A.P.); (M.J.); (K.S.); (E.V.); (K.L.)
- Centre of Excellence in Genomics and Translational Medicine, University of Tartu, 50090 Tartu, Estonia
| | - Kadri Seppa
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; (T.J.); (M.-A.P.); (M.J.); (K.S.); (E.V.); (K.L.)
- Centre of Excellence in Genomics and Translational Medicine, University of Tartu, 50090 Tartu, Estonia
- Laboratory Animal Centre, Institute of Biomedicine and Translational Medicine, University of Tartu, 14B Ravila Street, 50411 Tartu, Estonia
| | - Triin Tekko
- The Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal;
| | - Scott F. Gilbert
- Department of Biology, Swarthmore College, Swarthmore, PA 19081, USA;
| | - Eero Vasar
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; (T.J.); (M.-A.P.); (M.J.); (K.S.); (E.V.); (K.L.)
- Centre of Excellence in Genomics and Translational Medicine, University of Tartu, 50090 Tartu, Estonia
| | - Kersti Lilleväli
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, 19 Ravila Street, 50411 Tartu, Estonia; (T.J.); (M.-A.P.); (M.J.); (K.S.); (E.V.); (K.L.)
- Centre of Excellence in Genomics and Translational Medicine, University of Tartu, 50090 Tartu, Estonia
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Yu B, Zhou S, Yi S, Gu X. The regulatory roles of non-coding RNAs in nerve injury and regeneration. Prog Neurobiol 2015; 134:122-39. [PMID: 26432164 DOI: 10.1016/j.pneurobio.2015.09.006] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 08/20/2015] [Accepted: 09/05/2015] [Indexed: 12/16/2022]
Abstract
Non-coding RNAs (ncRNAs), especially microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), have attracted much attention since their regulatory roles in diverse cell processes were recognized. Emerging studies demonstrate that many ncRNAs are differentially expressed after injury to the nervous system, significantly affecting nerve regeneration. In this review, we compile the miRNAs and lncRNAs that have been reported to be dysregulated following a variety of central and peripheral nerve injuries, including acquired brain injury, spinal cord injury, and peripheral nerve injury. We also list investigations on how these miRNAs and lncRNAs exert the regulatory actions in neurodegenerative and neuroregenerative processes through different mechanisms involving their interaction with target coding genes. We believe that comprehension of the expression profiles and the possible functions of ncRNAs during the processes of nerve injury and regeneration will help understand the molecular mechanisms responsible for post-nerve-injury changes, and may contribute to the potential use of ncRNAs as a diagnostic marker and therapeutic target for nerve injury.
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Affiliation(s)
- Bin Yu
- Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, JS 226001, China
| | - Songlin Zhou
- Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, JS 226001, China
| | - Sheng Yi
- Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, JS 226001, China
| | - Xiaosong Gu
- Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, JS 226001, China.
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Sanz R, Ferraro GB, Fournier AE. IgLON cell adhesion molecules are shed from the cell surface of cortical neurons to promote neuronal growth. J Biol Chem 2014; 290:4330-42. [PMID: 25538237 DOI: 10.1074/jbc.m114.628438] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Matrix metalloproteinases and a disintegrin and metalloproteinases are members of the zinc endopeptidases, which cleave components of the extracellular matrix as well as cell surface proteins resulting in degradation or release of biologically active fragments. Surface ectodomain shedding affects numerous biological processes, including survival, axon outgrowth, axon guidance, and synaptogenesis. In this study, we evaluated the role of metalloproteinases in regulating cortical neurite growth. We found that treatment of mature cortical neurons with pan-metalloproteinase inhibitors or with tissue inhibitors of metalloproteinase-3 reduced neurite outgrowth. Through mass spectrometry, we characterized the metalloproteinase-sensitive cell surface proteome of mature cortical neurons. Members of the IgLON family of glycosylphosphatidylinositol-anchored neural cell adhesion molecules were identified and validated as proteins that were shed from the surface of mature cortical neurons in a metalloproteinase-dependent manner. Introduction of two members of the IgLON family, neurotrimin and NEGR1, in early embryonic neurons was sufficient to confer sensitivity to metalloproteinase inhibitors in neurite outgrowth assays. Outgrowth experiments on immobilized IgLON proteins revealed a role for all IgLON family members in promoting neurite extension from cortical neurons. Together, our findings support a role for metalloproteinase-dependent shedding of IgLON family members in regulating neurite outgrowth from mature cortical neurons.
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Affiliation(s)
- Ricardo Sanz
- From the Department of Neurology and Neurosurgery, Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Gino B Ferraro
- From the Department of Neurology and Neurosurgery, Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Alyson E Fournier
- From the Department of Neurology and Neurosurgery, Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada
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Yu B, Qian T, Wang Y, Zhou S, Ding G, Ding F, Gu X. miR-182 inhibits Schwann cell proliferation and migration by targeting FGF9 and NTM, respectively at an early stage following sciatic nerve injury. Nucleic Acids Res 2012; 40:10356-65. [PMID: 22917588 PMCID: PMC3488220 DOI: 10.1093/nar/gks750] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The regulation of Schwann cell (SC) responses to injury stimuli by microRNAs (miRNAs) remains to be explored. Here, we identified 17 miRNAs that showed dynamic expression alterations at five early time points following rat sciatic nerve resection. Then we analyzed the expression pattern of 17 miRNAs, and integrated their putative targets with differentially expressed mRNAs. The resulting 222 potential targets were mainly involved in cell phenotype modulation, including immune response, cell death and cell locomotion. Among 17 miRNAs, miR-182 expression was up-regulated. The enhanced expression of miR-182 was correlated with nerve injury-induced phenotype modulation of SCs. Further investigation revealed that fibroblast growth factor 9 (FGF9) and neurotrimin (NTM) were two direct targets of miR-182 in SCs, with miR-182 binding to the 3'-untranslated region of FGF9 and NTM. Silencing of FGF9 and NTM recapitulated the inhibiting effect of miR-182 mimics on SC proliferation and migration, respectively, whereas enforced knockdown of FGF9 and NTM reversed the promoting effect of miR-182 inhibitor on SC proliferation and migration, respectively. Our data indicate that nerve injury inhibits SC proliferation and migration through rapid regulation of miR-182 by targeting FGF9 and NTM, providing novel insights into the roles of miRNAs in nerve injury and repair.
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Affiliation(s)
- Bin Yu
- Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong 226001, China
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McNamee CJ, Youssef S, Moss D. IgLONs form heterodimeric complexes on forebrain neurons. Cell Biochem Funct 2011; 29:114-9. [PMID: 21321971 DOI: 10.1002/cbf.1730] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 12/16/2010] [Accepted: 12/20/2010] [Indexed: 11/07/2022]
Abstract
IgLONs are a family of four GPI-anchored cell adhesion molecules that regulate neurite outgrowth and synaptogenesis and may act as tumour suppressor genes. Recently we have proposed that two members of the IgLON family act as a heterodimeric complex termed DIgLON. Neurons isolated from chick forebrain co-express all six combinations of IgLONs and the intensity of fluorescence for each pair of IgLONs was highly correlated. Antibody-patching experiments on forebrain neurons show complex formation for IgLON pairs but not between unrelated GPI-anchored glycoproteins. Thus IgLONs are the first GPI-anchored family of glycoproteins shown to form heterodimeric complexes in the plane of the membrane.
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Mukhopadhyay P, Brock G, Pihur V, Webb C, Pisano MM, Greene RM. Developmental microRNA expression profiling of murine embryonic orofacial tissue. ACTA ACUST UNITED AC 2010; 88:511-34. [PMID: 20589883 DOI: 10.1002/bdra.20684] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Orofacial development is a multifaceted process involving precise, spatio-temporal expression of a panoply of genes. MicroRNAs (miRNAs), the largest family of noncoding RNAs involved in gene silencing, represent critical regulators of cell and tissue differentiation. MicroRNA gene expression profiling is an effective means of acquiring novel and valuable information regarding the expression and regulation of genes, under the control of miRNA, involved in mammalian orofacial development. METHODS To identify differentially expressed miRNAs during mammalian orofacial ontogenesis, miRNA expression profiles from gestation day (GD) -12, -13 and -14 murine orofacial tissue were compared utilizing miRXplore microarrays from Miltenyi Biotech. Quantitative real-time PCR was utilized for validation of gene expression changes. Cluster analysis of the microarray data was conducted with the clValid R package and the UPGMA clustering method. Functional relationships between selected miRNAs were investigated using Ingenuity Pathway Analysis. RESULTS Expression of over 26% of the 588 murine miRNA genes examined was detected in murine orofacial tissues from GD-12-GD-14. Among these expressed genes, several clusters were seen to be developmentally regulated. Differential expression of miRNAs within such clusters wereshown to target genes encoding proteins involved in cell proliferation, cell adhesion, differentiation, apoptosis and epithelial-mesenchymal transformation, all processes critical for normal orofacial development. CONCLUSIONS Using miRNA microarray technology, unique gene expression signatures of hundreds of miRNAs in embryonic orofacial tissue were defined. Gene targeting and functional analysis revealed that the expression of numerous protein-encoding genes, crucial to normal orofacial ontogeny, may be regulated by specific miRNAs.
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Affiliation(s)
- Partha Mukhopadhyay
- University of Louisville Birth Defects Center, Department of Molecular Cellular and Craniofacial Biology, ULSD, University of Louisville, Kentucky, USA
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