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Tomita T, Nakajima Y, Ohmiya Y, Miyazaki K. Novel three-dimensional live skin-like in vitro composite for bioluminescence reporter gene assay. FEBS J 2024. [PMID: 39148322 DOI: 10.1111/febs.17246] [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: 02/08/2024] [Revised: 05/20/2024] [Accepted: 08/02/2024] [Indexed: 08/17/2024]
Abstract
We genetically manipulated HaCaT cells, a spontaneously immortalised normal keratinocyte cell line, to stably express two different coloured luciferase reporter genes, driven by interleukin 8 (IL-8) and ubiquitin-C (UBC) promoters, respectively. Subsequently, we generated a three-dimensional (3D) skin-like in vitro composite (SLIC) utilising these cells, with the objective of monitoring bioluminescence emitted from the SLIC. This SLIC was generated on non-woven silica fibre membranes in differentiation medium. Immunohistochemical analyses of skin differentiation markers in the SLIC revealed the expression of keratins 2 and 10, filaggrin, and involucrin, indicating mature skin characteristics. This engineered SLIC was employed for real-time bioluminescence monitoring, allowing the assessment of time- and dose-dependent responses to UV stress, as well as to hydrophilic and hydrophobic chemical loads. Notably, evaluation of responses to hydrophobic substances has been challenging with conventional 2D cell culture methods, suggesting the need for a new approach, which this technology could address. Our observations suggest that engineered SLIC with constitutively expressing reporters driven by selected promoters which are tailored to specific objectives, significantly facilitates assays exploring the physiological functions of skin cells based on genetic response mechanisms. It also highlights new avenues for evaluating the physiological impacts of various compounds designed for topical application to human skin.
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Affiliation(s)
- Tatsunosuke Tomita
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Yoshihiro Nakajima
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Japan
| | - Yoshihiro Ohmiya
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Japan
- Osaka Institute of Technology (OIT), Omiya, Japan
| | - Koyomi Miyazaki
- Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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Duan C, Mooney T, Buerer L, Bowers C, Rong S, Kim SW, Fredericks AM, Monaghan SF, Fairbrother WG. The unusual gene architecture of polyubiquitin is created by dual-specific splice sites. Genome Biol 2024; 25:33. [PMID: 38268025 PMCID: PMC10809524 DOI: 10.1186/s13059-023-03157-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND The removal of introns occurs through the splicing of a 5' splice site (5'ss) with a 3' splice site (3'ss). These two elements are recognized by distinct components of the spliceosome. However, introns in higher eukaryotes contain many matches to the 5' and 3' splice-site motifs that are presumed not to be used. RESULTS Here, we find that many of these sites can be used. We also find occurrences of the AGGT motif that can function as either a 5'ss or a 3'ss-previously referred to as dual-specific splice sites (DSSs)-within introns. Analysis of the Sequence Read Archive reveals a 3.1-fold enrichment of DSSs relative to expectation, implying synergy between the ability to function as a 5'ss and 3'ss. Despite this suggested mechanistic advantage, DSSs are 2.7- and 4.7-fold underrepresented in annotated 5' and 3' splice sites. A curious exception is the polyubiquitin gene UBC, which contains a tandem array of DSSs that precisely delimit the boundary of each ubiquitin monomer. The resulting isoforms splice stochastically to include a variable number of ubiquitin monomers. We found no evidence of tissue-specific or feedback regulation but note the 8.4-fold enrichment of DSS-spliced introns in tandem repeat genes suggests a driving role in the evolution of genes like UBC. CONCLUSIONS We find an excess of unannotated splice sites and the utilization of DSSs in tandem repeats supports the role of splicing in gene evolution. These findings enhance our understanding of the diverse and complex nature of the splicing process.
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Affiliation(s)
- Chaorui Duan
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA
| | - Truman Mooney
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA
| | - Luke Buerer
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA
| | - Cory Bowers
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA
| | - Stephen Rong
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI, 02903, USA
| | - Seong Won Kim
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA
| | | | - Sean F Monaghan
- Division of Surgical Research, Department of Surgery, Alpert Medical School of Brown University/Rhode Island Hospital, Providence, RI, 02903, USA
| | - William G Fairbrother
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA.
- Center for Computational Molecular Biology, Brown University, Providence, RI, 02903, USA.
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Wang J, Zhang X, Zheng F, Yang Q, Bi F. Mitophagy-related long non-coding RNA signature predicts prognosis and drug response in Ovarian Cancer. J Ovarian Res 2023; 16:177. [PMID: 37633972 PMCID: PMC10463594 DOI: 10.1186/s13048-023-01247-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/24/2023] [Indexed: 08/28/2023] Open
Abstract
BACKGROUND Ovarian cancer (OC) is the most malignant tumor with the worst prognosis in female reproductive system. Mitophagy and long non-coding RNAs (lncRNAs) play pivotal roles in tumorigenesis, development, and drug resistance. The effects of mitophagy-related lncRNAs on OC prognosis and therapeutic response remain unelucidated. METHODS We retrieved OC-related RNA sequence, copy number variation, somatic mutation, and clinicopathological information from The Cancer Genome Atlas database and mitophagy-related gene sets from the Reactome database. Pearson's correlation analysis was used to distinguish mitophagy-related lncRNAs. A prognostic lncRNA signature was constructed using UniCox, LASSO, and forward stepwise regression analysis. Individuals with a risk score above or below the median were classified as high- or low-risk groups, respectively. The risk model was analyzed using the Kaplan-Meier estimator, receiver operating characteristic curve, decision curve analysis, and Cox regression analysis and validated using an internal dataset. LINC00174 was validated in clinical samples and OC cell lines. We also reviewed reports on the role of LINC00174 in cancer. Subsequently, a nomogram model was constructed. Furthermore, the Genomics of Drug Sensitivity in Cancer database was used to explore the relationship between the risk model and anti-tumor drug sensitivity. Gene set variation analysis was performed to assess potential differences in biological functions between the two groups. Finally, a lncRNA prognostic signature-related competing endogenous RNA (ceRNA) network was constructed. RESULTS The prognostic signature showed that patients in the high-risk group had a poorer prognosis. The nomogram exhibited satisfactory accuracy and predictive potential. LINC00174 mainly acts as an oncogene in cancer and is upregulated in OC; its knockdown inhibited the proliferation and migration, and promoted apoptosis of OC cells. High-risk patients were more insensitive to cisplatin and olaparib than low-risk patients. The ceRNA network may help explore the potential regulatory mechanisms of lncRNAs. CONCLUSION The mitophagy-related lncRNA signature can help estimate the survival and drug sensitivity, the ceRNA network may provide novel therapeutic targets for patients with OC.
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Affiliation(s)
- Jiao Wang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Heping District, Shenyang, 110004, China
| | - Xiaocui Zhang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Heping District, Shenyang, 110004, China
| | - Fei Zheng
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Heping District, Shenyang, 110004, China
| | - Qing Yang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Heping District, Shenyang, 110004, China.
| | - Fangfang Bi
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Heping District, Shenyang, 110004, China.
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Harshini V, Shukla N, Raval I, Kumar S, Shrivastava V, Patel AK, Joshi CG. Kidney transcriptome response to salinity adaptation in Labeo rohita. Front Physiol 2022; 13:991366. [PMID: 36311223 PMCID: PMC9606766 DOI: 10.3389/fphys.2022.991366] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/28/2022] [Indexed: 11/13/2022] Open
Abstract
The increasing salinization of freshwater resources, owing to global warming, has caused concern to freshwater aquaculturists. In this regard, the present study is aimed at economically important freshwater fish, L. rohita (rohu) adapting to varying degrees of salinity concentrations. The RNA-seq analysis of kidney tissue samples of L. rohita maintained at 2, 4, 6, and 8 ppt salinity was performed, and differentially expressed genes involved in various pathways were studied. A total of 755, 834, 738, and 716 transcripts were downregulated and 660, 926, 576, and 908 transcripts were up-regulated in 2, 4, 6, and 8 ppt salinity treatment groups, respectively, with reference to the control. Gene ontology enrichment analysis categorized the differentially expressed genes into 69, 154, 92, and 157 numbers of biological processes with the p value < 0.05 for 2, 4, 6, and 8 ppt salinity groups, respectively, based on gene functions. The present study found 26 differentially expressed solute carrier family genes involved in ion transportation and glucose transportation which play a significant role in osmoregulation. In addition, the upregulation of inositol-3-phosphate synthase 1A (INO1) enzyme indicated the role of osmolytes in salinity acclimatization of L. rohita. Apart from this, the study has also found a significant number of genes involved in the pathways related to salinity adaptation including energy metabolism, calcium ion regulation, immune response, structural reorganization, and apoptosis. The kidney transcriptome analysis elucidates a step forward in understanding the osmoregulatory process in L. rohita and their adaptation to salinity changes.
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Affiliation(s)
- Vemula Harshini
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Nitin Shukla
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Ishan Raval
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Sujit Kumar
- Postgraduate Institute of Fisheries Education and Research, Kamdhenu University, Himmatnagar, Gujarat, India
| | - Vivek Shrivastava
- Postgraduate Institute of Fisheries Education and Research, Kamdhenu University, Himmatnagar, Gujarat, India
| | - Amrutlal K. Patel
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
- *Correspondence: Amrutlal K. Patel, ; Chaitanya G. Joshi,
| | - Chaitanya G. Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
- *Correspondence: Amrutlal K. Patel, ; Chaitanya G. Joshi,
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Köhler SA, Brandl L, Strissel PL, Gloßner L, Ekici AB, Angeloni M, Ferrazzi F, Bahlinger V, Hartmann A, Beckmann MW, Eckstein M, Strick R. Improved Bladder Tumor RNA Isolation from Archived Tissues Using Methylene Blue for Normalization, Multiplex RNA Hybridization, Sequencing and Subtyping. Int J Mol Sci 2022; 23:ijms231810267. [PMID: 36142180 PMCID: PMC9499321 DOI: 10.3390/ijms231810267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/26/2022] [Accepted: 09/02/2022] [Indexed: 12/02/2022] Open
Abstract
Methylene blue (MB) is a dye used for histology with clinical importance and intercalates into nucleic acids. After MB staining of formalin fixed paraffin embedded (FFPE) muscle invasive bladder cancer (MIBC) and normal urothelium, specific regions could be microdissected. It is not known if MB influences RNA used for gene expression studies. Therefore, we analyzed MIBC using five different RNA isolation methods comparing patient matched FFPE and fresh frozen (FF) tissues pre-stained with or without MB. We demonstrate a positive impact of MB on RNA integrity with FF tissues using real time PCR with no interference of its chemical properties. FFPE tissues showed no improvement of RNA integrity, which we propose is due to formalin induced nucleotide crosslinks. Using direct multiplex RNA hybridization the best genes for normalization of MIBC and control tissues were identified from 34 reference genes. In addition, 5SrRNA and 5.8SrRNA were distinctive reference genes detecting <200 bp fragments important for mRNA analyses. Using these normalized RNAs from MB stained MIBC and applying multiplex RNA hybridization and mRNA sequencing, a minimal gene expression panel precisely identified luminal and basal MIBC tumor subtypes, important for diagnosis, prognosis and chemotherapy response.
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Affiliation(s)
- Stefanie A. Köhler
- Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
| | - Lisa Brandl
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Pamela L. Strissel
- Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Laura Gloßner
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Arif B. Ekici
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Miriam Angeloni
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Fulvia Ferrazzi
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
- Department of Nephropathology, Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Veronika Bahlinger
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Arndt Hartmann
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Matthias W. Beckmann
- Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
| | - Markus Eckstein
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054 Erlangen, Germany
| | - Reiner Strick
- Laboratory for Molecular Medicine, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Universitaetsstrasse 21-23, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), University Hospital Erlangen, Östliche Stadtmauerstrasse 30, 91054 Erlangen, Germany
- Correspondence: ; Tel.: +49-91318536671
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Dong R, Gao S, Shan MJ. Identification of the similarly expressed genes in patients with polycystic ovary syndrome and transsexuals. Medicine (Baltimore) 2021; 100:e26990. [PMID: 34477128 PMCID: PMC8415929 DOI: 10.1097/md.0000000000026990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/18/2021] [Accepted: 07/15/2021] [Indexed: 11/27/2022] Open
Abstract
ABSTRACT Polycystic ovary syndrome (PCOS) is a common female infertility, which may be caused by excessive androgen, but its mechanism remains unknown. Transsexuals are women who take androgen drugs for a long time, and gradually have male signs. Their ovaries may have received high concentrations of androgen, which leads to the failure of ovarian reproductive function. Therefore, we searched the relevant data of PCOS and transsexuals in gene expression omnibus database, used limma package to identify the most similarly genes, and then analyzed the possible mechanism of PCOS through gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathway analysis. Then, the protein-protein interaction network was constructed by searching the String database, and the top 5 hub genes were identified by the cytohubba plug-in of Cytoscape. Finally, ubiquitin conjugating enzyme E2 E1 (UBE2E1), ubiquitin C (UBC), transcription elongation factor B subunit 1 (TCEB1), ubiquitin conjugating enzyme E2 N (UBE2N), and ring finger protein 7 (RNF7) genes were identified as the most similarly expressed genes between PCOS and Transsexuals. They may cause the ubiquitination of androgen receptor and eventually lead to sinus follicular growth arrest. In conclusion, 5 Central genes were identified in PCOS and transsexuals. These genes can be used as targets for early diagnosis or treatment of PCOS.
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Affiliation(s)
- Rong Dong
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine & National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, No. 88 Changling Road, Xiqing District, Tianjin, China
| | - Shang Gao
- Jilin University, Bethune Second Clinical Medical College, 218 Ziqiang street, Nanguan District Changchun, China
| | - Meng-Jie Shan
- Department of Plastic Surgery, Peking Union Medical College Hospital, Beijing, China
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Bettencourt C, Miki Y, Piras IS, de Silva R, Foti SC, Talboom JS, Revesz T, Lashley T, Balazs R, Viré E, Warner TT, Huentelman MJ, Holton JL. MOBP and HIP1 in multiple system atrophy: New α-synuclein partners in glial cytoplasmic inclusions implicated in the disease pathogenesis. Neuropathol Appl Neurobiol 2021; 47:640-652. [PMID: 33368549 PMCID: PMC8219819 DOI: 10.1111/nan.12688] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/16/2020] [Accepted: 12/14/2020] [Indexed: 01/02/2023]
Abstract
AIMS Multiple system atrophy (MSA) is a fatal neurodegenerative disease. Similar to Parkinson's disease (PD), MSA is an α-synucleinopathy, and its pathological hallmark consists of glial cytoplasmic inclusions (GCIs) containing α-synuclein (SNCA) in oligodendrocytes. We previously identified consistent changes in myelin-associated oligodendrocyte basic protein (MOBP) and huntingtin interacting protein 1 (HIP1) DNA methylation status in MSA. We hypothesized that if differential DNA methylation at these loci is mechanistically relevant for MSA, it should have downstream consequences on gene regulation. METHODS We investigated the relationship between MOBP and HIP1 DNA methylation and mRNA levels in cerebellar white matter from MSA and healthy controls. Additionally, we analysed protein expression using western blotting, immunohistochemistry and proximity ligation assays. RESULTS We found decreased MOBP mRNA levels significantly correlated with increased DNA methylation in MSA. For HIP1, we found a distinct relationship between DNA methylation and gene expression levels in MSA compared to healthy controls, suggesting this locus may be subjected to epigenetic remodelling in MSA. Although soluble protein levels for MOBP and HIP1 in cerebellar white matter were not significantly different between MSA cases and controls, we found striking differences between MSA and other neurodegenerative diseases, including PD and Huntington's disease. We also found that MOBP and HIP1 are mislocalized into the GCIs in MSA, where they appear to interact with SNCA. CONCLUSIONS This study supports a role for DNA methylation in downregulation of MOBP mRNA in MSA. Most importantly, the identification of MOBP and HIP1 as new constituents of GCIs emphasizes the relevance of these two loci to the pathogenesis of MSA.
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Affiliation(s)
- Conceição Bettencourt
- Queen Square Brain Bank for Neurological DisordersUCL Queen Square Institute of NeurologyLondonUK
- Department of Clinical and Movement NeurosciencesUCL Queen Square Institute of NeurologyLondonUK
| | - Yasuo Miki
- Queen Square Brain Bank for Neurological DisordersUCL Queen Square Institute of NeurologyLondonUK
- Department of NeuropathologyInstitute of Brain ScienceHirosaki University Graduate School of MedicineHirosakiJapan
| | - Ignazio S. Piras
- Neurogenomics DivisionTranslational Genomics Research InstitutePhoenixAZUSA
| | - Rohan de Silva
- Department of Clinical and Movement NeurosciencesUCL Queen Square Institute of NeurologyLondonUK
- Reta Lila Weston InstituteUCL Queen Square Institute of NeurologyLondonUK
| | - Sandrine C. Foti
- Queen Square Brain Bank for Neurological DisordersUCL Queen Square Institute of NeurologyLondonUK
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyLondonUK
| | - Joshua S. Talboom
- Neurogenomics DivisionTranslational Genomics Research InstitutePhoenixAZUSA
| | - Tamas Revesz
- Queen Square Brain Bank for Neurological DisordersUCL Queen Square Institute of NeurologyLondonUK
- Reta Lila Weston InstituteUCL Queen Square Institute of NeurologyLondonUK
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyLondonUK
| | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological DisordersUCL Queen Square Institute of NeurologyLondonUK
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyLondonUK
| | - Robert Balazs
- Queen Square Brain Bank for Neurological DisordersUCL Queen Square Institute of NeurologyLondonUK
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyLondonUK
| | | | - Thomas T. Warner
- Queen Square Brain Bank for Neurological DisordersUCL Queen Square Institute of NeurologyLondonUK
- Department of Clinical and Movement NeurosciencesUCL Queen Square Institute of NeurologyLondonUK
- Reta Lila Weston InstituteUCL Queen Square Institute of NeurologyLondonUK
| | - Matt J. Huentelman
- Neurogenomics DivisionTranslational Genomics Research InstitutePhoenixAZUSA
| | - Janice L. Holton
- Queen Square Brain Bank for Neurological DisordersUCL Queen Square Institute of NeurologyLondonUK
- Department of Clinical and Movement NeurosciencesUCL Queen Square Institute of NeurologyLondonUK
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Abstract
Ubiquitin (Ub) is one of the proteins that are highly conserved from yeast to humans. It is an essential core unit of the well-defined post-translational modification, called ubiquitination, which is involved in a variety of biological processes. In meta-zoans, Ub is encoded by two monoubiquitin genes and two polyubiquitin genes, in which a single Ub is fused to a ribosomal protein or Ub coding units are arranged in tandem repeats. In mice, polyubiquitin genes (Ubb and Ubc) play a pivotal role to meet the requirement of cellular Ub pools during embryonic development. In addition, expression levels of polyubiquitin genes are increased to adapt to environmental stimuli such as oxidative, heat-shock, and proteotoxic stress. Several researchers have reported about the perturbation of Ub pools through genetic alteration or exogenous Ub delivery using diverse model systems. To study Ub pool changes in a physiologically relevant manner, changing Ub pools via the regulation of endogenous polyubiquitin gene expression has recently been introduced. Furthermore, to understand the regulation of polyubiquitin gene expression more precisely, cis-acting elements and trans-acting factors, which are regulatory components of polyubiquitin genes, have been analyzed. In this review, we discuss how the role of polyu-biquitin genes has been studied during the past decade, es-pecially focusing on their regulation.
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Affiliation(s)
- Seung-Woo Han
- Department of Life Science, University of Seoul, Seoul 02504, Korea
| | - Byung-Kwon Jung
- Department of Life Science, University of Seoul, Seoul 02504, Korea
| | - Kwon-Yul Ryu
- Department of Life Science, University of Seoul, Seoul 02504, Korea
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Kawalerski RR, Leach SD, Escobar-Hoyos LF. Pancreatic cancer driver mutations are targetable through distant alternative RNA splicing dependencies. Oncotarget 2021; 12:525-533. [PMID: 33796221 PMCID: PMC7984828 DOI: 10.18632/oncotarget.27901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/03/2021] [Indexed: 12/16/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC), the most common histological subtype of pancreatic cancer, has one of the highest case fatality rates of all known solid malignancies. Over the past decade, several landmark studies have established mutations in KRAS and TP53 as the predominant drivers of PDAC pathogenesis and therapeutic resistance, though treatment options for PDACs and other tumors with these mutations remain extremely limited. Hampered by late tumor discovery and diagnosis, clinicians are often faced with using aggressive and non-specific chemotherapies to treat advanced disease. Clinically meaningful responses to targeted therapy are often limited to the minority of patients with susceptible PDACs, and immunotherapies have routinely encountered roadblocks in effective activation of tumor-infiltrating immune cells. Alternative RNA splicing (ARS) has recently gained traction in the PDAC literature as a field from which we may better understand and treat complex mechanisms of PDAC initiation, progression, and therapeutic resistance. Here, we review PDAC pathogenesis as it relates to fundamental ARS biology, with an extension to implications for PDAC patient clinical management.
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Affiliation(s)
- Ryan R. Kawalerski
- Medical Scientist Training Program, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Steven D. Leach
- Departments of Molecular and Systems Biology, Surgery, and Medicine, Dartmouth Geisel School of Medicine and Norris Cotton Cancer Center, Lebanon, NH 03766, USA
| | - Luisa F. Escobar-Hoyos
- Department of Therapeutic Radiology, Yale University, New Haven, CT 06513, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06513, USA
- Department of Pathology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY 11794, USA
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Zamai L. Unveiling Human Non-Random Genome Editing Mechanisms Activated in Response to Chronic Environmental Changes: I. Where Might These Mechanisms Come from and What Might They Have Led To? Cells 2020; 9:E2362. [PMID: 33121045 PMCID: PMC7693803 DOI: 10.3390/cells9112362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/18/2020] [Accepted: 10/19/2020] [Indexed: 12/13/2022] Open
Abstract
This article challenges the notion of the randomness of mutations in eukaryotic cells by unveiling stress-induced human non-random genome editing mechanisms. To account for the existence of such mechanisms, I have developed molecular concepts of the cell environment and cell environmental stressors and, making use of a large quantity of published data, hypothesised the origin of some crucial biological leaps along the evolutionary path of life on Earth under the pressure of natural selection, in particular, (1) virus-cell mating as a primordial form of sexual recombination and symbiosis; (2) Lamarckian CRISPR-Cas systems; (3) eukaryotic gene development; (4) antiviral activity of retrotransposon-guided mutagenic enzymes; and finally, (5) the exaptation of antiviral mutagenic mechanisms to stress-induced genome editing mechanisms directed at "hyper-transcribed" endogenous genes. Genes transcribed at their maximum rate (hyper-transcribed), yet still unable to meet new chronic environmental demands generated by "pollution", are inadequate and generate more and more intronic retrotransposon transcripts. In this scenario, RNA-guided mutagenic enzymes (e.g., Apolipoprotein B mRNA editing catalytic polypeptide-like enzymes, APOBECs), which have been shown to bind to retrotransposon RNA-repetitive sequences, would be surgically targeted by intronic retrotransposons on opened chromatin regions of the same "hyper-transcribed" genes. RNA-guided mutagenic enzymes may therefore "Lamarkianly" generate single nucleotide polymorphisms (SNP) and gene copy number variations (CNV), as well as transposon transposition and chromosomal translocations in the restricted areas of hyper-functional and inadequate genes, leaving intact the rest of the genome. CNV and SNP of hyper-transcribed genes may allow cells to surgically explore a new fitness scenario, which increases their adaptability to stressful environmental conditions. Like the mechanisms of immunoglobulin somatic hypermutation, non-random genome editing mechanisms may generate several cell mutants, and those codifying for the most environmentally adequate proteins would have a survival advantage and would therefore be Darwinianly selected. Non-random genome editing mechanisms represent tools of evolvability leading to organismal adaptation including transgenerational non-Mendelian gene transmission or to death of environmentally inadequate genomes. They are a link between environmental changes and biological novelty and plasticity, finally providing a molecular basis to reconcile gene-centred and "ecological" views of evolution.
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Affiliation(s)
- Loris Zamai
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; ; Tel./Fax: +39-0722-304-319
- National Institute for Nuclear Physics (INFN)-Gran Sasso National Laboratory (LNGS), 67100 Assergi, L’Aquila, Italy
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Moon CI, Tompkins W, Wang Y, Godec A, Zhang X, Pipkorn P, Miller CA, Dehner C, Dahiya S, Hirbe AC. Unmasking Intra-tumoral Heterogeneity and Clonal Evolution in NF1-MPNST. Genes (Basel) 2020; 11:genes11050499. [PMID: 32369930 PMCID: PMC7291009 DOI: 10.3390/genes11050499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/19/2020] [Accepted: 04/30/2020] [Indexed: 12/15/2022] Open
Abstract
Sarcomas are highly aggressive cancers that have a high propensity for metastasis, fail to respond to conventional therapies, and carry a poor 5-year survival rate. This is particularly true for patients with neurofibromatosis type 1 (NF1), in which 8%–13% of affected individuals will develop a malignant peripheral nerve sheath tumor (MPNST). Despite continued research, no effective therapies have emerged from recent clinical trials based on preclinical work. One explanation for these failures could be the lack of attention to intra-tumoral heterogeneity. Prior studies have relied on a single sample from these tumors, which may not be representative of all subclones present within the tumor. In the current study, samples were taken from three distinct areas within a single tumor from a patient with an NF1-MPNST. Whole exome sequencing, RNA sequencing, and copy number analysis were performed on each sample. A blood sample was obtained as a germline DNA control. Distinct mutational signatures were identified in different areas of the tumor as well as significant differences in gene expression among the spatially distinct areas, leading to an understanding of the clonal evolution within this patient. These data suggest that multi-regional sampling may be important for driver gene identification and biomarker development in the future.
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Affiliation(s)
- Chang-In Moon
- Division of Medical Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; (C.-I.M.); (Y.W.); (X.Z.)
| | - William Tompkins
- Washington University School of Medicine, St. Louis, MO 63110, USA;
| | - Yuxi Wang
- Division of Medical Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; (C.-I.M.); (Y.W.); (X.Z.)
| | - Abigail Godec
- College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA;
| | - Xiaochun Zhang
- Division of Medical Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; (C.-I.M.); (Y.W.); (X.Z.)
| | - Patrik Pipkorn
- Department of Otolaryngology, Division of Head and Neck Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA;
- Siteman Cancer Center, St. Louis, MO 63110, USA; (C.A.M.); (S.D.)
| | - Christopher A. Miller
- Siteman Cancer Center, St. Louis, MO 63110, USA; (C.A.M.); (S.D.)
- McDonnell Genome Institute, Division of Oncology—Stem Cell Biology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carina Dehner
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA;
| | - Sonika Dahiya
- Siteman Cancer Center, St. Louis, MO 63110, USA; (C.A.M.); (S.D.)
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA;
| | - Angela C. Hirbe
- Division of Medical Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; (C.-I.M.); (Y.W.); (X.Z.)
- Siteman Cancer Center, St. Louis, MO 63110, USA; (C.A.M.); (S.D.)
- Correspondence: ; Tel.: +1-314-747-3096
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