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Drazdauskienė U, Kapustina Ž, Medžiūnė J, Dubovskaja V, Sabaliauskaitė R, Jarmalaitė S, Lubys A. Fusion sequencing via terminator-assisted synthesis (FTAS-seq) identifies TMPRSS2 fusion partners in prostate cancer. Mol Oncol 2023; 17:993-1006. [PMID: 37300660 DOI: 10.1002/1878-0261.13428] [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: 10/28/2022] [Revised: 02/26/2023] [Accepted: 04/03/2023] [Indexed: 06/12/2023] Open
Abstract
Genetic rearrangements that fuse an androgen-regulated promoter area with a protein-coding portion of an originally androgen-unaffected gene are frequent in prostate cancer, with the fusion between transmembrane serine protease 2 (TMPRSS2) and ETS transcription factor ERG (ERG) (TMPRSS2-ERG fusion) being the most prevalent. Conventional hybridization- or amplification-based methods can test for the presence of expected gene fusions, but the exploratory analysis of currently unknown fusion partners is often cost-prohibitive. Here, we developed an innovative next-generation sequencing (NGS)-based approach for gene fusion analysis termed fusion sequencing via terminator-assisted synthesis (FTAS-seq). FTAS-seq can be used to enrich the gene of interest while simultaneously profiling the whole spectrum of its 3'-terminal fusion partners. Using this novel semi-targeted RNA-sequencing technique, we were able to identify 11 previously uncharacterized TMPRSS2 fusion partners and capture a range of TMPRSS2-ERG isoforms. We tested the performance of FTAS-seq with well-characterized prostate cancer cell lines and utilized the technique for the analysis of patient RNA samples. FTAS-seq chemistry combined with appropriate primer panels holds great potential as a tool for biomarker discovery that can support the development of personalized cancer therapies.
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Affiliation(s)
| | | | | | | | | | - Sonata Jarmalaitė
- National Cancer Institute, Vilnius, Lithuania
- Institute of Biosciences, Life Sciences Center, Vilnius University, Lithuania
| | - Arvydas Lubys
- Thermo Fisher Scientific Baltics, Vilnius, Lithuania
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2
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Verploegh ISC, Conidi A, Brouwer RWW, Balcioglu HE, Karras P, Makhzami S, Korporaal A, Marine JC, Lamfers M, Van IJcken WFJ, Leenstra S, Huylebroeck D. Comparative single-cell RNA-sequencing profiling of BMP4-treated primary glioma cultures reveals therapeutic markers. Neuro Oncol 2022; 24:2133-2145. [PMID: 35639831 PMCID: PMC9713526 DOI: 10.1093/neuonc/noac143] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Glioblastoma (GBM) is the most aggressive primary brain tumor. Its cellular composition is very heterogeneous, with cells exhibiting stem-cell characteristics (GSCs) that co-determine therapy resistance and tumor recurrence. Bone Morphogenetic Protein (BMP)-4 promotes astroglial and suppresses oligodendrocyte differentiation in GSCs, processes associated with superior patient prognosis. We characterized variability in cell viability of patient-derived GBM cultures in response to BMP4 and, based on single-cell transcriptome profiling, propose predictive positive and early-response markers for sensitivity to BMP4. METHODS Cell viability was assessed in 17 BMP4-treated patient-derived GBM cultures. In two cultures, one highly-sensitive to BMP4 (high therapeutic efficacy) and one with low-sensitivity, response to treatment with BMP4 was characterized. We applied single-cell RNA-sequencing, analyzed the relative abundance of cell clusters, searched for and identified the aforementioned two marker types, and validated these results in all 17 cultures. RESULTS High variation in cell viability was observed after treatment with BMP4. In three cultures with highest sensitivity for BMP4, a substantial new cell subpopulation formed. These cells displayed decreased cell proliferation and increased apoptosis. Neuronal differentiation was reduced most in cultures with little sensitivity for BMP4. OLIG1/2 levels were found predictive for high sensitivity to BMP4. Activation of ribosomal translation (RPL27A, RPS27) was up-regulated within one day in cultures that were very sensitive to BMP4. CONCLUSION The changes in composition of patient-derived GBM cultures obtained after treatment with BMP4 correlate with treatment efficacy. OLIG1/2 expression can predict this efficacy, and upregulation of RPL27A and RPS27 are useful early-response markers.
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Affiliation(s)
| | | | - Rutger W W Brouwer
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Center for Biomics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Hayri E Balcioglu
- Department of Medical Oncology, Erasmus Medical Center Cancer Institute, Rotterdam, The Netherlands
| | | | - Samira Makhzami
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Anne Korporaal
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Martine Lamfers
- Department of Neurosurgery, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wilfred F J Van IJcken
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sieger Leenstra
- Department of Neurosurgery, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Danny Huylebroeck
- Corresponding Author: Danny Huylebroeck, Department of Cell Biology, Erasmus University Medical Center, Building Ee, room Ee-1040b, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands ()
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3
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C1orf61 promotes hepatocellular carcinoma metastasis and increases the therapeutic response to sorafenib. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119048. [PMID: 33915231 DOI: 10.1016/j.bbamcr.2021.119048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 04/16/2021] [Accepted: 04/22/2021] [Indexed: 12/12/2022]
Abstract
C1orf61 is a specific transcriptional activator that is highly up-regulated during weeks 4-9 of human embryogenesis, the period in which most organs develop. We have previously demonstrated that C1orf61 acts as a tumor activator in human hepatocellular carcinoma (HCC) tumorigenesis and metastasis. However, the underlying molecular mechanisms of tumor initiation and progression in HCC remain obscure. In this study, we demonstrated that the pattern of C1orf61 expression was closely correlated with metastasis in liver cancer cells. Gene expression profiling analysis indicated that C1orf61 regulated diverse genes related to cell growth, migration, invasion and epithelial-mesenchymal transition (EMT). Results showed that C1orf61 promotes hepatocellular carcinoma metastasis by inducing cellular EMT in vivo and in vitro. Moreover, C1orf61-induced cellular EMT and migration are involved in the activation of the STAT3 and Akt cascade pathways. In addition, C1orf61 expression improved the efficacy of the anticancer therapy sorafenib in HCC patients. For the first time, we report a regulatory pathway by which C1orf61 promoted cancer cell metastasis and regulated the therapeutic response to sorafenib. These findings increased our understanding of the molecular events that regulate metastasis and treatment in HCC.
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4
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Eze UC, Bhaduri A, Haeussler M, Nowakowski TJ, Kriegstein AR. Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia. Nat Neurosci 2021; 24:584-594. [PMID: 33723434 PMCID: PMC8012207 DOI: 10.1038/s41593-020-00794-1] [Citation(s) in RCA: 189] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/23/2020] [Indexed: 01/31/2023]
Abstract
The human cortex comprises diverse cell types that emerge from an initially uniform neuroepithelium that gives rise to radial glia, the neural stem cells of the cortex. To characterize the earliest stages of human brain development, we performed single-cell RNA-sequencing across regions of the developing human brain, including the telencephalon, diencephalon, midbrain, hindbrain and cerebellum. We identify nine progenitor populations physically proximal to the telencephalon, suggesting more heterogeneity than previously described, including a highly prevalent mesenchymal-like population that disappears once neurogenesis begins. Comparison of human and mouse progenitor populations at corresponding stages identifies two progenitor clusters that are enriched in the early stages of human cortical development. We also find that organoid systems display low fidelity to neuroepithelial and early radial glia cell types, but improve as neurogenesis progresses. Overall, we provide a comprehensive molecular and spatial atlas of early stages of human brain and cortical development.
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Affiliation(s)
- Ugomma C Eze
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Aparna Bhaduri
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco (UCSF), San Francisco, CA, USA.
| | | | - Tomasz J Nowakowski
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA
- Department of Anatomy, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Arnold R Kriegstein
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco (UCSF), San Francisco, CA, USA.
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5
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Vrabec K, Boštjančič E, Koritnik B, Leonardis L, Dolenc Grošelj L, Zidar J, Rogelj B, Glavač D, Ravnik-Glavač M. Differential Expression of Several miRNAs and the Host Genes AATK and DNM2 in Leukocytes of Sporadic ALS Patients. Front Mol Neurosci 2018; 11:106. [PMID: 29670510 PMCID: PMC5893848 DOI: 10.3389/fnmol.2018.00106] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 03/19/2018] [Indexed: 12/12/2022] Open
Abstract
Genetic studies have managed to explain many cases of familial amyotrophic lateral sclerosis (ALS) through mutations in several genes. However, the cause of a majority of sporadic cases remains unknown. Recently, epigenetics, especially miRNA studies, show some promising aspects. We aimed to evaluate the differential expression of 10 miRNAs, including miR-9, miR-338, miR-638, miR-663a, miR-124a, miR-143, miR-451a, miR-132, miR-206, and let-7b, for which some connection to ALS was shown previously in ALS culture cells, animal models or patients, and in three miRNA host genes, including C1orf61 (miR-9), AATK (miR-338), and DNM2 (miR-638), in leukocyte samples of 84 patients with sporadic ALS. We observed significant aberrant dysregulation across our patient cohort for miR-124a, miR-206, miR-9, let-7b, and miR-638. Since we did not use neurological controls we cannot rule out that the revealed differences in expression of investigated miRNAs are specific for ALS. Nevertheless, the group of these five miRNAs is worth of additional research in leukocytes of larger cohorts from different populations in order to verify their potential association to ALS disease. We also detected a significant up-regulation of the AAKT gene and down-regulation of the DNM2 gene, and thus, for the first time, we connected these with sporadic ALS cases. These findings open up new research toward miRNAs as diagnostic biomarkers and epigenetic processes involved in ALS. The detected significant deregulation of AAKT and DNM2 in sporadic ALS also represents an interesting finding. The DNM2 gene was previously found to be mutated in Charcot-Marie-Tooth neuropathy-type CMT2M and centronuclear myopathy (CNM). In addition, as recent studies connected AATK and frontotemporal dementia (FTD) and DNM2 and hereditary spastic paraplegia (HSP), these two genes together with our results genetically connect, at least in part, five diseases, including FTD, HSP, Charcot-Marie-Tooth (type CMT2M), CNM, and ALS, thus opening future research toward a better understanding of the cell biology involved in these partly overlapping pathologies.
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Affiliation(s)
- Katarina Vrabec
- Department of Molecular Genetics, Faculty of Medicine, Institute of Pathology, University of Ljubljana, Ljubljana, Slovenia
| | - Emanuela Boštjančič
- Department of Molecular Genetics, Faculty of Medicine, Institute of Pathology, University of Ljubljana, Ljubljana, Slovenia
| | - Blaž Koritnik
- Division of Neurology, Institute of Clinical Neurophysiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Lea Leonardis
- Division of Neurology, Institute of Clinical Neurophysiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Leja Dolenc Grošelj
- Division of Neurology, Institute of Clinical Neurophysiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Janez Zidar
- Division of Neurology, Institute of Clinical Neurophysiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Boris Rogelj
- Department of Biotechnology, Jožef Štefan Institute, Ljubljana, Slovenia.,Biomedical Research Institute, Ljubljana, Slovenia
| | - Damjan Glavač
- Department of Molecular Genetics, Faculty of Medicine, Institute of Pathology, University of Ljubljana, Ljubljana, Slovenia
| | - Metka Ravnik-Glavač
- Department of Molecular Genetics, Faculty of Medicine, Institute of Pathology, University of Ljubljana, Ljubljana, Slovenia.,Faculty of Medicine, Institute of Biochemistry, University of Ljubljana, Ljubljana, Slovenia
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6
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Tarui T, Kim A, Flake A, McClain L, Stratigis JD, Fried I, Newman R, Slonim DK, Bianchi DW. Amniotic fluid transcriptomics reflects novel disease mechanisms in fetuses with myelomeningocele. Am J Obstet Gynecol 2017; 217:587.e1-587.e10. [PMID: 28735706 DOI: 10.1016/j.ajog.2017.07.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND Cell-free RNA in amniotic fluid supernatant reflects developmental changes in gene expression in the living fetus, which includes genes that are specific to the central nervous system. Although it has been previously shown that central nervous system-specific transcripts are present in amniotic fluid supernatant, it is not known whether changes in the amniotic fluid supernatant transcriptome reflect the specific pathophysiologic condition of fetal central nervous system disorders. In myelomeningocele, there is open communication between the central nervous system and amniotic fluid. OBJECTIVES The purpose of this study was to identify molecular pathophysiologic changes and novel disease mechanisms that are specific to myelomeningocele by the analysis of amniotic fluid supernatant cell-free RNA in fetuses with open myelomeningocele. STUDY DESIGN Amniotic fluid supernatant was collected from 10 pregnant women at the time of the open myelomeningocele repair in the second trimester (24.5±1.0 weeks); 10 archived amniotic fluid supernatant from sex and gestational age-matched euploid fetuses without myelomeningocele were used as controls (20.9±0.9 weeks). Differentially regulated gene expression patterns were analyzed with the use of human genome expression arrays. RESULTS Fetuses with myelomeningocele had 284 differentially regulated genes (176 up- and 108 down-regulated) in amniotic fluid supernatant. Known genes that were associated with myelomeningocele (PRICKLE2, GLI3, RAB23, HES1, FOLR1) and novel dysregulated genes were identified in association with neurodevelopment and neuronal regeneration (up-regulated, GAP43 and ZEB1) or axonal growth and guidance (down-regulated, ACAP1). Pathway analysis demonstrated a significant contribution of inflammation to disease and a broad influence of Wnt signaling pathways (Wnt1, Wnt5A, ITPR1). CONCLUSION Transcriptomic analyses of living fetuses with myelomeningocele with the use of amniotic fluid supernatant cell-free RNA demonstrated differential regulation of specific genes and molecular pathways relevant to this central nervous system disorder, which resulted in a new understanding of pathophysiologic changes. The data also suggested the importance of pathways that involve secondary disease, such as inflammation, in myelomeningocele. These newly identified pathways may lead to hypotheses that can test novel therapeutic targets as adjuncts to fetal surgical repair.
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Kalantari P, Harandi OF, Agarwal S, Rus F, Kurt-Jones EA, Fitzgerald KA, Caffrey DR, Golenbock DT. miR-718 represses proinflammatory cytokine production through targeting phosphatase and tensin homolog (PTEN). J Biol Chem 2017; 292:5634-5644. [PMID: 28209713 DOI: 10.1074/jbc.m116.749325] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 02/10/2017] [Indexed: 01/04/2023] Open
Abstract
Bacterial sepsis involves a complex interaction between the host immune response and bacterial LPS. LPS binds Toll-like receptor (TLR) 4, which leads to the release of proinflammatory cytokines that are essential for a potent innate immune response against pathogens. The innate immune system is tightly regulated, as excessive inflammation can lead to organ failure and death. MicroRNAs have recently emerged as important regulators of the innate immune system. Here we determined the function of miR-718, which is conserved across mammals and overlaps with the 5' UTR of the interleukin 1 receptor-associated kinase (IRAK1) gene. As IRAK1 is a key component of innate immune signaling pathways that are downstream of most TLRs, we hypothesized that miR-718 helps regulate the innate immune response. Activation of TLR4, but not TLR3, induced the expression of miR-718 in macrophages. miR-718 expression was also induced in the spleens of mice upon LPS injection. miR-718 modulates PI3K/Akt signaling by directly down-regulating phosphatase and tensin homolog (PTEN), thereby promoting phosphorylation of Akt, which leads to a decrease in proinflammatory cytokine production. Phosphorylated Akt induces let-7e expression, which, in turn, down-regulates TLR4 and further diminishes TLR4-mediated proinflammatory signals. Decreased miR-718 expression is associated with bacterial burden during Neisseria gonorrhoeae infection and alters the infection dynamics of N. gonorrhoeae in vitro Furthermore, miR-718 regulates the induction of LPS tolerance in macrophages. We propose a role for miR-718 in controlling TLR4 signaling and inflammatory cytokine signaling through a negative feedback regulation loop involving down-regulation of TLR4, IRAK1, and NF-κB.
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Affiliation(s)
- Parisa Kalantari
- From the Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 and
| | - Omid F Harandi
- the Department of Medicine, Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215
| | - Sarika Agarwal
- From the Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 and
| | - Florentina Rus
- From the Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 and
| | - Evelyn A Kurt-Jones
- From the Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 and
| | - Katherine A Fitzgerald
- From the Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 and
| | - Daniel R Caffrey
- From the Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 and
| | - Douglas T Golenbock
- From the Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 and
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8
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Pandruvada SN, Gonzalez OA, Kirakodu S, Gudhimella S, Stromberg AJ, Ebersole JL, Orraca L, Gonzalez-Martinez J, Novak MJ, Huja SS. Bone biology-related gingival transcriptome in ageing and periodontitis in non-human primates. J Clin Periodontol 2016; 43:408-17. [PMID: 26859687 DOI: 10.1111/jcpe.12528] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2016] [Indexed: 12/11/2022]
Abstract
AIM Cellular and molecular immunoinflammatory changes in gingival tissues drive alveolar bone loss in periodontitis. Since ageing is a risk factor for periodontitis, we sought to identify age-related gingival transcriptome changes associated with bone metabolism in both healthy and in naturally occurring periodontitis. MATERIALS AND METHODS Adult (12-16 years) and aged (18-23 years) non-human primates (M. mulatta) (n = 24) were grouped into healthy and periodontitis. Gingival tissue samples were obtained and subjected to microarray analysis using the Gene Chip Macaque Genome Array. Gene expression profiles involved in osteoclast/osteoblast proliferation, adhesion and function were evaluated and compared across and between the age groups. QPCR was also performed on selected genes to validate microarray data. RESULTS Healthy aged tissues showed a gene profile expression that suggest enhancement of osteoclastic adhesion, proliferation/survival and function (SPP1, TLR4, MMP8 and TFEC) and impaired osteoblastic activity (SMEK3P and SMAD5). The gingival transcriptome in both adult and aged animals with naturally occurring periodontitis (FOS, IL6, TLR4, MMP9, MMP10 and SPP1 genes) was consistent with a local inflammatory response driving towards bone/connective tissue destruction. CONCLUSION A pro-osteoclastogenic gingival transcriptome is associated with periodontitis irrespective of age; however; a greater bone-destructive molecular environment is associated with ageing in healthy tissues.
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Affiliation(s)
- Subramanya N Pandruvada
- Division of Orthodontics, College of Dentistry, University of Kentucky, Lexington, KY, USA.,Center for Oral Health Research, College of Dentistry, University of Kentucky, Lexington, KY, USA
| | - Octavio A Gonzalez
- Center for Oral Health Research, College of Dentistry, University of Kentucky, Lexington, KY, USA
| | - Sreenatha Kirakodu
- Center for Oral Health Research, College of Dentistry, University of Kentucky, Lexington, KY, USA
| | - Sudha Gudhimella
- Division of Orthodontics, College of Dentistry, University of Kentucky, Lexington, KY, USA
| | | | - Jeffrey L Ebersole
- Center for Oral Health Research, College of Dentistry, University of Kentucky, Lexington, KY, USA
| | - Luis Orraca
- School of Dental Medicine, University of Puerto Rico, San Juan, PR, USA
| | | | - Michael J Novak
- Center for Oral Health Research, College of Dentistry, University of Kentucky, Lexington, KY, USA
| | - Sarandeep S Huja
- Division of Orthodontics, College of Dentistry, University of Kentucky, Lexington, KY, USA.,Center for Oral Health Research, College of Dentistry, University of Kentucky, Lexington, KY, USA
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Chen X, Yao P, Chu X, Hao L, Guo X, Xu B. Isolation of arginine kinase from Apis cerana cerana and its possible involvement in response to adverse stress. Cell Stress Chaperones 2015; 20:169-83. [PMID: 25135575 PMCID: PMC4255252 DOI: 10.1007/s12192-014-0535-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 08/03/2014] [Accepted: 08/05/2014] [Indexed: 02/04/2023] Open
Abstract
Arginine kinases (AK) in invertebrates play the same role as creatine kinases in vertebrates. Both proteins are important for energy metabolism, and previous studies on AK focused on this attribute. In this study, the arginine kinase gene was isolated from Apis cerana cerana and was named AccAK. A 5'-flanking region was also cloned and shown to contain abundant putative binding sites for transcription factors related to development and response to adverse stress. We imitated several abiotic and biotic stresses suffered by A. cerana cerana during their life, including heavy metals, pesticides, herbicides, heat, cold, oxidants, antioxidants, ecdysone, and Ascosphaera apis and then studied the expression patterns of AccAK after these treatments. AccAK was upregulated under all conditions, and, in some conditions, this response was very pronounced. Western blot and AccAK enzyme activity assays confirmed the results. In addition, a disc diffusion assay showed that overexpression of AccAK reduced the resistance of Escherichia coli cells to multiple adverse stresses. Taken together, our results indicated that AccAK may be involved of great significance in response to adverse abiotic and biotic stresses.
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Affiliation(s)
- Xiaobo Chen
- />State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018 People’s Republic of China
| | - Pengbo Yao
- />State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018 People’s Republic of China
| | - Xiaoqian Chu
- />State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018 People’s Republic of China
| | - Lili Hao
- />State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018 People’s Republic of China
| | - Xingqi Guo
- />State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018 People’s Republic of China
| | - Baohua Xu
- />College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong 271018 People’s Republic of China
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10
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Identification and characterization of an Apis cerana cerana Delta class glutathione S-transferase gene (AccGSTD) in response to thermal stress. Naturwissenschaften 2012; 100:153-63. [DOI: 10.1007/s00114-012-1006-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 11/18/2012] [Accepted: 12/06/2012] [Indexed: 01/21/2023]
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11
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Hu HM, Chen Y, Liu L, Zhang CG, Wang W, Gong K, Huang Z, Guo MX, Li WX, Li W. C1orf61 acts as a tumor activator in human hepatocellular carcinoma and is associated with tumorigenesis and metastasis. FASEB J 2012; 27:163-73. [PMID: 23012322 DOI: 10.1096/fj.12-216622] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The genomic amplification of chromosome 1q long arm, the chromosomal region containing C1orf61, is a common event in human cancers. However, the expression pattern of chromosome 1 open reading frame 61 (C1orf61) in hepatocellular carcinoma (HCC) and its effects on HCC progression remain unclear. We have previously reported that C1orf61 is highly up-regulated during human embryogenesis. In this study, we report that C1orf61 expression is associated with the progression of liver disease. We found that C1orf61 is up-regulated in hepatic cirrhosis tissues and is further up-regulated in primary HCC tumors. Moreover, hepatitis B virus (HBV)-positive patients exhibited significantly higher levels of C1orf61 expression than HBV-negative patients. The evaluation of highly malignant HCC cell lines revealed high protein expression levels of C1orf61. Furthermore, the C1orf61 protein was found to be predominantly distributed within the cytoplasm. The ectopic expression of C1orf61 in the nonmalignant L02 cell line promoted cellular proliferation and colony formation in vitro, as well as cell cycle progression via the regulation of the expression of specific cell cycle-related proteins. In addition, the overexpression of C1orf61 in L02 cells facilitated cellular invasion and metastasis. The down-regulation of epithelial markers (E-cadherin and occludin) and the up-regulation of mesenchymal markers (N-cadherin, vimentin, and snail) suggested that the overexpression of C1orf61 induced the epithelial-mesenchymal transition (EMT) that is linked to metastasis. Taken together, our findings demonstrate, for the first time, the roles of C1orf61 in HCC tumorigenesis and metastasis.
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Affiliation(s)
- Hai-Ming Hu
- College of Life Sciences, Wuhan University, Wuhan, China
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12
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Abstract
Since its discovery 25 years ago, nuclear factor-κB (NF-κB) has emerged as a transcription factor that controls diverse biological functions, ranging from inflammation to learning and memory. Activation of NF-κB initiates an elaborate genetic program. Some of the NF-κB-driven genes do not encode proteins but rather are precursors to microRNAs. These microRNAs play important roles in the regulation of the inflammatory process, some being inhibitory and others activating. Here, we discuss both the regulation of their expression and the function of some of these non-coding RNA genes. We also include a personal discussion of how NF-κB was first discovered.
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Affiliation(s)
- Mark P Boldin
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
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13
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Meng F, Lu W, Yu F, Kang M, Guo X, Xu B. Ribosomal protein L11 is related to brain maturation during the adult phase in Apis cerana cerana (Hymenoptera, Apidae). Naturwissenschaften 2012; 99:343-52. [PMID: 22415557 DOI: 10.1007/s00114-012-0905-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 02/26/2012] [Accepted: 02/28/2012] [Indexed: 01/25/2023]
Abstract
Ribosomal proteins (RPs) play pivotal roles in developmental regulation. The loss or mutation of ribosomal protein L11 (RPL11) induces various developmental defects. However, few RPs have been functionally characterized in Apis cerana cerana. In this study, we isolated a single copy gene, AccRPL11, and characterized its connection to brain maturation. AccRPL11 expression was highly concentrated in the adult brain and was significantly induced by abiotic stresses such as pesticides and heavy metals. Immunofluorescence assays demonstrated that AccRPL11 was localized to the medulla, lobula and surrounding tissues of esophagus in the brain. The post-transcriptional knockdown of AccRPL11 gene expression resulted in a severe decrease in adult brain than in other tissues. The expression levels of other brain development-related genes, p38, ERK2, CacyBP and CREB, were also reduced. Immunofluorescence signal attenuation was also observed in AccRPL11-rich regions of the brain in dsAccRPL11-injected honeybees. Taken together, these results suggest that AccRPL11 may be functional in brain maturation in honeybee adults.
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Affiliation(s)
- Fei Meng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, People's Republic of China
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Negative regulation of TLR4 via targeting of the proinflammatory tumor suppressor PDCD4 by the microRNA miR-21. Nat Immunol 2009; 106:5282-7. [PMID: 19946272 DOI: 10.1073/pnas.0810909106] [Citation(s) in RCA: 459] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The tumor suppressor PDCD4 is a proinflammatory protein that promotes activation of the transcription factor NF-kappaB and suppresses interleukin 10 (IL-10). Here we found that mice deficient in PDCD4 were protected from lipopolysaccharide (LPS)-induced death. The induction of NF-kappaB and IL-6 by LPS required PDCD4, whereas LPS enhanced IL-10 induction in cells lacking PDCD4. Treatment of human peripheral blood mononuclear cells with LPS resulted in lower PDCD4 expression, which was due to induction of the microRNA miR-21 via the adaptor MyD88 and NF-kappaB. Transfection of cells with a miR-21 precursor blocked NF-kappaB activity and promoted IL-10 production in response to LPS, whereas transfection with antisense oligonucleotides to miR-21 or targeted protection of the miR-21 site in Pdcd4 mRNA had the opposite effect. Thus, miR-21 regulates PDCD4 expression after LPS stimulation.
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Gorodkin J, Cirera S, Hedegaard J, Gilchrist MJ, Panitz F, Jørgensen C, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, Rosenkilde C, Wang J, Li H, Li R, Liu B, Hu S, Dong W, Li W, Yu J, Wang J, Stærfeldt HH, Wernersson R, Madsen LB, Thomsen B, Hornshøj H, Bujie Z, Wang X, Wang X, Bolund L, Brunak S, Yang H, Bendixen C, Fredholm M. Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. Genome Biol 2007; 8:R45. [PMID: 17407547 PMCID: PMC1895994 DOI: 10.1186/gb-2007-8-4-r45] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Revised: 01/18/2007] [Accepted: 04/02/2007] [Indexed: 12/05/2022] Open
Abstract
A resource consisting of one million porcine ESTs is described, providing an essential resource for annotation, comparative genomics, assembly of the pig genome sequence, and further porcine transcription studies. Background Knowledge of the structure of gene expression is essential for mammalian transcriptomics research. We analyzed a collection of more than one million porcine expressed sequence tags (ESTs), of which two-thirds were generated in the Sino-Danish Pig Genome Project and one-third are from public databases. The Sino-Danish ESTs were generated from one normalized and 97 non-normalized cDNA libraries representing 35 different tissues and three developmental stages. Results Using the Distiller package, the ESTs were assembled to roughly 48,000 contigs and 73,000 singletons, of which approximately 25% have a high confidence match to UniProt. Approximately 6,000 new porcine gene clusters were identified. Expression analysis based on the non-normalized libraries resulted in the following findings. The distribution of cluster sizes is scaling invariant. Brain and testes are among the tissues with the greatest number of different expressed genes, whereas tissues with more specialized function, such as developing liver, have fewer expressed genes. There are at least 65 high confidence housekeeping gene candidates and 876 cDNA library-specific gene candidates. We identified differential expression of genes between different tissues, in particular brain/spinal cord, and found patterns of correlation between genes that share expression in pairs of libraries. Finally, there was remarkable agreement in expression between specialized tissues according to Gene Ontology categories. Conclusion This EST collection, the largest to date in pig, represents an essential resource for annotation, comparative genomics, assembly of the pig genome sequence, and further porcine transcription studies.
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Affiliation(s)
- Jan Gorodkin
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Susanna Cirera
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Jakob Hedegaard
- Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, Blichers Alle, DK-8830 Tjele, Denmark
| | - Michael J Gilchrist
- The Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge, CB2 1QN, UK
| | - Frank Panitz
- Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, Blichers Alle, DK-8830 Tjele, Denmark
| | - Claus Jørgensen
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Karsten Scheibye-Knudsen
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Troels Arvin
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Steen Lumholdt
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Milena Sawera
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Trine Green
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Bente J Nielsen
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Jakob H Havgaard
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Carina Rosenkilde
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
| | - Jun Wang
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
- Institute of Human Genetics, University of Aarhus, Nordre Ringgade 1, DK-8000 Aarhus C, Denmark
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campus Vej 55, DK-5230 Odense M, Denmark
| | - Heng Li
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
- Institute of Human Genetics, University of Aarhus, Nordre Ringgade 1, DK-8000 Aarhus C, Denmark
| | - Ruiqiang Li
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campus Vej 55, DK-5230 Odense M, Denmark
| | - Bin Liu
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
| | - Songnian Hu
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
| | - Wei Dong
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
| | - Wei Li
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
| | - Jun Yu
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
| | - Jian Wang
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
| | - Hans-Henrik Stærfeldt
- Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, DK-2800 Lyngby, Denmark
| | - Rasmus Wernersson
- Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, DK-2800 Lyngby, Denmark
| | - Lone B Madsen
- Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, Blichers Alle, DK-8830 Tjele, Denmark
| | - Bo Thomsen
- Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, Blichers Alle, DK-8830 Tjele, Denmark
| | - Henrik Hornshøj
- Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, Blichers Alle, DK-8830 Tjele, Denmark
| | - Zhan Bujie
- Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, Blichers Alle, DK-8830 Tjele, Denmark
| | - Xuegang Wang
- Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, Blichers Alle, DK-8830 Tjele, Denmark
| | - Xuefei Wang
- Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, Blichers Alle, DK-8830 Tjele, Denmark
| | - Lars Bolund
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
- Institute of Human Genetics, University of Aarhus, Nordre Ringgade 1, DK-8000 Aarhus C, Denmark
| | - Søren Brunak
- Center for Biological Sequence Analysis, BioCentrum-DTU, Building 208, DK-2800 Lyngby, Denmark
| | - Huanming Yang
- Beijing Genomics Institute, The Airport Industrial Road, Beijing 101300, PR China
| | - Christian Bendixen
- Department of Genetics and Biotechnology, Danish Institute of Agricultural Sciences, Blichers Alle, DK-8830 Tjele, Denmark
| | - Merete Fredholm
- Division of Genetics and Bioinformatics, IBHV, Grønnegärdsvej 3, The Royal Veterinary and Agricultural University, DK-1870 Frederiksberg C, Denmark
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Feig C, Kirchhoff C, Ivell R, Naether O, Schulze W, Spiess AN. A new paradigm for profiling testicular gene expression during normal and disturbed human spermatogenesis. ACTA ACUST UNITED AC 2006; 13:33-43. [PMID: 17114209 DOI: 10.1093/molehr/gal097] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The aim of this study was to identify gene expression patterns of the testis that correlate with the appearance of distinct stages of male germ cells. We avoided the pitfalls of mixed pathological phenotypes of the testis and circumvented the inapplicability of using the first spermatogenic wave as done previously on rodents. This was accomplished by using 28 samples showing defined and highly homogeneous pathologies selected from 578 testicular biopsies obtained from 289 men with azoospermia (two biopsies each). The molecular signature of the different developmental stages correlated with the morphological preclassification of the testicular biopsies, as shown by resampling-based hierarchical clustering using different measures of variability. By using analysis of variance (ANOVA) and extensive permutation analysis, we filtered 1181 genes that exhibit exceptional statistical significance in testicular expression and grouped subsets with transcriptional changes within the pre-meiotic (348 genes), post-meiotic (81 genes) and terminal differentiation (38 genes) phase. Several distinct molecular classes, metabolic pathways and transcription factor binding sites are involved, depending on the transcriptional profile of the gene clusters that were built using a novel clustering procedure based on not only similarity but also statistical significance.
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Affiliation(s)
- C Feig
- Department of Andrology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
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Capes-Davis A, Tolhurst O, Dunn JM, Jeffrey PL. Expression of doublecortin (DCX) and doublecortin-like kinase (DCLK) within the developing chick brain. Dev Dyn 2005; 232:457-67. [PMID: 15614772 DOI: 10.1002/dvdy.20240] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Doublecortin (DCX) is a microtubule-associated protein widely expressed in the developing mammalian nervous system and important for neuronal migration. DCX is known to belong to a novel protein family defined by sequence homology and the presence of a conserved microtubule-binding domain, but the functions of other members of this family are still undefined. In this study, we describe the cloning of the chick ortholog of doublecortin-like kinase (DCLK), a member of this family, and assess the expression of DCX and DCLK in the layered regions of the developing chick brain. DCX and DCLK are widely expressed in pallial and subpallial structures, including the telencephalon, optic tectum, and cerebellum, in similar distribution patterns. In addition to their expression in migrating cells, both proteins were also detected in the ventricular zone and in postmigratory Purkinje cells. Finally, DCX and DCLK were found to be coexpressed in all areas examined. In postmigratory Purkinje cells, DCX and DCLK both colocalized to the cell membrane, although DCLK was also distributed more generally throughout the cell soma. These data are consistent with multiple roles for DCX and DCLK in the developing chicken brain and suggest that the chick cerebellum will be an intriguing system to explore the effects of DCX and DCLK on postmigratory neuronal function.
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Philips ST, Albin RL, Martin DM. Genetics of subthalamic nucleus in development and disease. Exp Neurol 2005; 192:320-30. [PMID: 15755549 DOI: 10.1016/j.expneurol.2004.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2004] [Revised: 11/05/2004] [Accepted: 11/09/2004] [Indexed: 11/16/2022]
Abstract
The subthalamic nucleus (STN) is a crucial node in the basal ganglia. Clinical success in targeting the STN for deep brain stimulation in Parkinson's disease patients has prompted increased interest in understanding STN biology. In this report, we discuss recent evidence for transcription factor mediated regulation of STN development. We also review STN developmental neurobiology and known patterns of gene expression in the developing and mature STN.
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Affiliation(s)
- Steven T Philips
- Department of Pediatrics, The University of Michigan, Ann Arbor, MI 48109, USA
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Baskerville S, Bartel DP. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA (NEW YORK, N.Y.) 2005; 11:241-7. [PMID: 15701730 PMCID: PMC1370713 DOI: 10.1261/rna.7240905] [Citation(s) in RCA: 1088] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
MicroRNAs (miRNAs) are short endogenous RNAs known to post-transcriptionally repress gene expression in animals and plants. A microarray profiling survey revealed the expression patterns of 175 human miRNAs across 24 different human organs. Our results show that proximal pairs of miRNAs are generally coexpressed. In addition, an abrupt transition in the correlation between pairs of expressed miRNAs occurs at a distance of 50 kb, implying that miRNAs separated by <50 kb typically derive from a common transcript. Some microRNAs are within the introns of host genes. Intronic miRNAs are usually coordinately expressed with their host gene mRNA, implying that they also generally derive from a common transcript, and that in situ analyses of host gene expression can be used to probe the spatial and temporal localization of intronic miRNAs.
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Affiliation(s)
- Scott Baskerville
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
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