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Mukhopadhyay P, Smolenkova I, Seelan RS, Pisano MM, Greene RM. Spatiotemporal Expression and Functional Analysis of miRNA-22 in the Developing Secondary Palate. Cleft Palate Craniofac J 2023; 60:27-38. [PMID: 34730446 DOI: 10.1177/10556656211054004] [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] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE Normal development of the embryonic orofacial region requires precise spatiotemporal coordination between numerous genes. MicroRNAs represent small, single-stranded, non-coding molecules that regulate gene expression. This study examines the role of microRNA-22 (miR-22) in murine orofacial ontogeny. METHODS Spatiotemporal and differential expression of miR-22 (mmu-miR-22-3p) within the developing secondary palate was determined by in situ hybridization and quantitative real-time PCR, respectively. Bioinformatic approaches were used to predict potential mRNA targets of miR-22 and analyze their association with cellular functions indispensable for normal orofacial ontogeny. An in vitro palate organ culture system was used to assess the role of miR-22 in secondary palate development. RESULTS There was a progressive increase in miR-22 expression from GD12.5 to GD14.5 in palatal processes. On GD12.5 and GD13.5, miR-22 was expressed in the future oral, nasal, and medial edge epithelia. On GD14.5, miR-22 expression was observed in the residual midline epithelial seam (MES), the nasal epithelium and the mesenchyme, but not in the oral epithelium. Inhibition of miR-22 activity in palate organ cultures resulted in failure of MES removal. Bioinformatic analyses revealed potential mRNA targets of miR-22 that may play significant roles in regulating apoptosis, migration, and/or convergence/extrusion, developmental processes that modulate MES removal during palatogenesis. CONCLUSIONS Results from the current study suggest a key role for miR-22 in the removal of the MES during palatogenesis and that miR-22 may represent a potential contributor to the etiology of cleft palate.
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Affiliation(s)
- Partha Mukhopadhyay
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, School of Dentistry, 5170University of Louisville, Louisville, KY 40202
| | - Irina Smolenkova
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, School of Dentistry, 5170University of Louisville, Louisville, KY 40202
| | - Ratnam S Seelan
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, School of Dentistry, 5170University of Louisville, Louisville, KY 40202
| | - M Michele Pisano
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, School of Dentistry, 5170University of Louisville, Louisville, KY 40202
| | - Robert M Greene
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, School of Dentistry, 5170University of Louisville, Louisville, KY 40202
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Wang K, Donnarumma F, Herke SW, Dong C, Herke PF, Murray KK. RNA sampling from tissue sections using infrared laser ablation. Anal Chim Acta 2019; 1063:91-98. [PMID: 30967191 DOI: 10.1016/j.aca.2019.02.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/17/2019] [Accepted: 02/24/2019] [Indexed: 10/27/2022]
Abstract
RNA was obtained from discrete locations of frozen rat brain tissue sections through infrared (IR) laser ablation using a 3-μm wavelength in transmission geometry. The ablated plume was captured in a microcentrifuge tube containing RNAse-free buffer and processed using a commercial RNA purification kit. RNA transfer efficiency and integrity were evaluated based on automated electrophoresis in microfluidic chips. Reproducible IR-laser ablation of intact RNA was demonstrated with purified RNA at laser fluences of 3-5 kJ/m2 (72 ± 12% transfer efficiency) and with tissue sections at a laser fluence of 13 kJ/m2 (79 ± 14% transfer efficiency); laser energies were attenuated ∼20% by the soda-lime glass slides used to support the samples. RNA integrity from tissue ablation was >90% of its original RIN value (∼7) and the purified RNA was sufficiently intact for conversion to cDNA and subsequent qPCR assay.
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Affiliation(s)
- Kelin Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Scott W Herke
- Genomics Facility, College of Science, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Chao Dong
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Patrick F Herke
- Genomics Facility, College of Science, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, United States.
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Mukhopadhyay P, Smolenkova I, Warner D, Pisano MM, Greene RM. Spatio-Temporal Expression and Functional Analysis of miR-206 in Developing Orofacial Tissue. Microrna 2019; 8:43-60. [PMID: 30068287 DOI: 10.2174/2211536607666180801094528] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/28/2018] [Accepted: 07/27/2018] [Indexed: 01/24/2023]
Abstract
BACKGROUND Development of the mammalian palate is dependent on precise, spatiotemporal expression of a panoply of genes. MicroRNAs (miRNAs), the largest family of noncoding RNAs, function as crucial modulators of cell and tissue differentiation, regulating expression of key downstream genes. OBSERVATIONS Our laboratory has previously identified several developmentally regulated miRNAs, including miR-206, during critical stages of palatal morphogenesis. The current study reports spatiotemporal distribution of miR-206 during development of the murine secondary palate (gestational days 12.5-14.5). RESULT AND CONCLUSION Potential cellular functions and downstream gene targets of miR-206 were investigated using functional assays and expression profiling, respectively. Functional analyses highlighted potential roles of miR-206 in governing TGFß- and Wnt signaling in mesenchymal cells of the developing secondary palate. In addition, altered expression of miR-206 within developing palatal tissue of TGFß3-/- fetuses reinforced the premise that crosstalk between this miRNA and TGFß3 is crucial for secondary palate development.
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Affiliation(s)
- Partha Mukhopadhyay
- Division of Craniofacial Development and Anomalies, Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY 40202, United States
| | - Irina Smolenkova
- Division of Craniofacial Development and Anomalies, Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY 40202, United States
| | - Dennis Warner
- Division of Craniofacial Development and Anomalies, Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY 40202, United States
| | - Michele M Pisano
- Division of Craniofacial Development and Anomalies, Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY 40202, United States
| | - Robert M Greene
- Division of Craniofacial Development and Anomalies, Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY 40202, United States
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Abstract
The purpose of this chapter is to provide a step-by-step protocol to enable performance of laser capture microdissection (LCM) on tissue sections from mammalian embryos or postnatal organism stages in order to collect pure populations of neural crest cells from which sufficient amounts of nucleic acids and/or protein can be obtained for quantitative analysis. The methods (1) define a strategy to genetically and indelibly label mammalian neural crest-derived cells with a fluorescent marker, thus enabling their isolation throughout the pre- and postnatal life span of the organism, and (2) describe subsequent isolation by LCM of the labeled neural crest cells, or their derivatives, from embryonic/postnatal tissue cryosections. Details are provided for using the Arcturus PixCell®IIe Laser Capture Microdissection System (Arcturus) and CapSure LCM Caps (Thermo Fisher Scientific), to which the selected cells adhere upon laser-mediated capture. The protocol outlined herein can be applied in any situation wherein limited cellular samples are available for isolation by LCM. Nucleic acids or proteins can be extracted from LCM-isolated cells and processed for high-density gene expression profiling analyses (microarrays or RNA sequencing), Real-Time PCR (q-PCR) for specific candidate gene expression, investigation of DNA methylation, as well as for varied protein analyses.
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Sarkar S, Alam N, Mandal SS, Chatterjee K, Ghosh S, Roychoudhury S, Panda CK. Differential transmission of the molecular signature of RBSP3, LIMD1 and CDC25A in basal/ parabasal versus spinous of normal epithelium during head and neck tumorigenesis: A mechanistic study. PLoS One 2018; 13:e0195937. [PMID: 29672635 PMCID: PMC5909606 DOI: 10.1371/journal.pone.0195937] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/03/2018] [Indexed: 12/16/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a global disease and mortality burden, necessitating the elucidation of its molecular progression for effective disease management. The study aims to understand the molecular profile of three candidate cell cycle regulatory genes, RBSP3, LIMD1 and CDC25A in the basal/ parabasal versus spinous layer of normal oral epithelium and during head and neck tumorigenesis. Immunohistochemical expression and promoter methylation was used to determine the molecular signature in normal oral epithelium. The mechanism of alteration transmission of this profile during tumorigenesis was then explored through additional deletion and mutation in HPV/ tobacco etiological groups, followed byclinico-pathological correlation. In basal/parabasal layer, the molecular signature of the genes was low protein expression/ high promoter methylation of RBSP3, high expression/ low methylation of LIMD1 and high expression of CDC25A. Dysplastic epithelium maintained the signature of RBSP3 through high methylation/ additional deletion with loss of the signatures of LIMD1 and CDC25A via deletion/ additional methylation. Similarly, maintenance and / or loss of signature in invasive tumors was by recurrent deletion/ methylation. Thus, differential patterns of alteration of the genes might be pre-requisite for the development of dysplastic and invasive lesions. Etiological factors played a key role in promoting genetic alterations and determining prognosis. Tobacco negative HNSCC patients had significantly lower alterations of LIMD1 and CDC25A, along with better survival among tobacco negative/ HPV positive patients. Our data suggests the necessity for perturbation of normal molecular profile of RBSP3, LIMD1 and CDC25A in conjunction with etiological factors for head and neck tumorigenesis, implying their diagnostic and prognostic significance.
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Affiliation(s)
- Shreya Sarkar
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, Kolkata, India
| | - Neyaz Alam
- Department of Surgical Oncology, Chittaranjan National Cancer Institute, Kolkata, India
| | - Syam Sundar Mandal
- Department of Epidemiology and Biostatistics, Chittaranjan National Cancer Institute, Kolkata, India
| | - Kabita Chatterjee
- Department of Oral and Maxillofacial Pathology, Buddha Institute of Dental Sciences and Hospital, Patna, India
| | - Supratim Ghosh
- Department of Oral and Maxillofacial Pathology, Burdwan Dental College and Hospital, Burdwan, India
| | - Susanta Roychoudhury
- Basic Research, Saroj Gupta Cancer Centre and Research Institute, Kolkata, India
| | - Chinmay Kumar Panda
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, Kolkata, India
- * E-mail:
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Kummari E, Guo-Ross SX, Eells JB. Laser capture microdissection--a demonstration of the isolation of individual dopamine neurons and the entire ventral tegmental area. J Vis Exp 2015:e52336. [PMID: 25742438 PMCID: PMC4354571 DOI: 10.3791/52336] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Laser capture microdissection (LCM) is used to isolate a concentrated population of individual cells or precise anatomical regions of tissue from tissue sections on a microscope slide. When combined with immunohistochemistry, LCM can be used to isolate individual cells types based on a specific protein marker. Here, the LCM technique is described for collecting a specific population of dopamine neurons directly labeled with tyrosine hydroxylase immunohistochemistry and for isolation of the dopamine neuron containing region of the ventral tegmental area using indirect tyrosine hydroxylase immunohistochemistry on a section adjacent to those used for LCM. An infrared (IR) capture laser is used to both dissect individual neurons as well as the ventral tegmental area off glass slides and onto an LCM cap for analysis. Complete dehydration of the tissue with 100% ethanol and xylene is critical. The combination of the IR capture laser and the ultraviolet (UV) cutting laser is used to isolate individual dopamine neurons or the ventral tegmental area when using PEN membrane slides. A PEN membrane slide has significant advantages over a glass slide as it offers better consistency in capturing and collecting cells, is faster collecting large pieces of tissue, is less reliant on dehydration and results in complete removal of the tissue from the slide. Although removal of large areas of tissue from a glass slide is feasible, it is considerably more time consuming and frequently leaves some residual tissue behind. Data shown here demonstrate that RNA of sufficient quantity and quality can be obtained using these procedures for quantitative PCR measurements. Although RNA and DNA are the most commonly isolated molecules from tissue and cells collected with LCM, isolation and measurement of microRNA, protein and epigenetic changes in DNA can also benefit from the enhanced anatomical and cellular resolution obtained using LCM.
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Affiliation(s)
- Evangel Kummari
- Department of Basic Sciences, Mississippi State University College of Veterinary Medicine
| | - Shirley X Guo-Ross
- Department of Basic Sciences, Mississippi State University College of Veterinary Medicine
| | - Jeffrey B Eells
- Department of Basic Sciences, Mississippi State University College of Veterinary Medicine;
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