1
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Conway JR, Gillani R, Crowdis J, Reardon B, Park J, Han S, Titchen B, Benamar M, Haq R, Van Allen EM. Somatic structural variants drive distinct modes of oncogenesis in melanoma. J Clin Invest 2024; 134:e177270. [PMID: 38758740 PMCID: PMC11213511 DOI: 10.1172/jci177270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/07/2024] [Indexed: 05/19/2024] Open
Abstract
The diversity of structural variants (SVs) in melanoma and how they impact oncogenesis are incompletely known. We performed harmonized analysis of SVs across melanoma histologic and genomic subtypes, and we identified distinct global properties between subtypes. These included the frequency and size of SVs and SV classes, their relation to chromothripsis events, and the impact on cancer-related genes of SVs that alter topologically associated domain (TAD) boundaries. Following our prior identification of double-stranded break repair deficiency in a subset of triple-wild-type cutaneous melanoma, we identified MRE11 and NBN loss-of-function SVs in melanomas with this mutational signature. Experimental knockouts of MRE11 and NBN, followed by olaparib cell viability assays in melanoma cells, indicated that dysregulation of each of these genes may cause sensitivity to PARP inhibitors in cutaneous melanomas. Broadly, harmonized analysis of melanoma SVs revealed distinct global genomic properties and molecular drivers, which may have biological and therapeutic impact.
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Affiliation(s)
- Jake R. Conway
- Division of Medical Sciences, Harvard University, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Riaz Gillani
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Jett Crowdis
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Brendan Reardon
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jihye Park
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Seunghun Han
- Division of Medical Sciences, Harvard University, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Breanna Titchen
- Division of Medical Sciences, Harvard University, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Rizwan Haq
- Center for Cancer Precision Medicine and
| | - Eliezer M. Van Allen
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Center for Cancer Precision Medicine and
- Parker Institute for Cancer Immunotherapy, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
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2
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Wei X, Yu S, Zhang T, Liu L, Wang X, Wang X, Chan YS, Wang Y, Meng S, Chen YG. MicroRNA-200 Loaded Lipid Nanoparticles Promote Intestinal Epithelium Regeneration in Canonical MicroRNA-Deficient Mice. ACS NANO 2023; 17:22901-22915. [PMID: 37939210 PMCID: PMC10690841 DOI: 10.1021/acsnano.3c08030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/10/2023]
Abstract
Intestinal epithelium undergoes regeneration after injuries, and the disruption of this process can lead to inflammatory bowel disease and tumorigenesis. Intestinal stem cells (ISCs) residing in the crypts are crucial for maintaining the intestinal epithelium's homeostasis and promoting regeneration upon injury. However, the precise role of DGCR8, a critical component in microRNA (miRNA) biogenesis, in intestinal regeneration remains poorly understood. In this study, we provide compelling evidence demonstrating the indispensable role of epithelial miRNAs in the regeneration of the intestine in mice subjected to 5-FU or irradiation-induced injury. Through a comprehensive pooled screen of miRNA function in Dgcr8-deficient organoids, we observe that the loss of the miR-200 family leads to the hyperactivation of the p53 pathway, thereby reducing ISCs and impairing epithelial regeneration. Notably, downregulation of the miR-200 family and hyperactivation of the p53 pathway are verified in colonic tissues from patients with active ulcerative colitis (UC). Most importantly, the transient supply of miR-200 through the oral delivery of lipid nanoparticles (LNPs) carrying miR-200 restores ISCs and promotes intestinal regeneration in mice following acute injury. Our study implies the miR-200/p53 pathway as a promising therapeutic target for active UC patients with diminished levels of the miR-200 family. Furthermore, our findings suggest that the clinical application of LNP-miRNAs could enhance the efficacy, safety, and acceptability of existing therapeutic modalities for intestinal diseases.
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Affiliation(s)
- Xiyang Wei
- Guangzhou
Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou
National Laboratory, Guangzhou 510005, China
| | - Shicheng Yu
- Guangzhou
Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou
National Laboratory, Guangzhou 510005, China
| | | | - Liansheng Liu
- Guangzhou
Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou
National Laboratory, Guangzhou 510005, China
| | - Xu Wang
- Guangzhou
National Laboratory, Guangzhou 510005, China
| | - Xiaodan Wang
- The
State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for
Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yun-Shen Chan
- Guangzhou
National Laboratory, Guangzhou 510005, China
| | - Yangming Wang
- Institute
of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Shu Meng
- Guangzhou
National Laboratory, Guangzhou 510005, China
| | - Ye-Guang Chen
- Guangzhou
National Laboratory, Guangzhou 510005, China
- The
State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for
Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- School
of Basic Medicine, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
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3
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Tao S, Xie SJ, Diao LT, Lv G, Hou YR, Hu YX, Xu WY, Du B, Xiao ZD. RNA-binding protein CCDC137 activates AKT signaling and promotes hepatocellular carcinoma through a novel non-canonical role of DGCR8 in mRNA localization. J Exp Clin Cancer Res 2023; 42:194. [PMID: 37542342 PMCID: PMC10403887 DOI: 10.1186/s13046-023-02749-3] [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: 05/17/2023] [Accepted: 07/04/2023] [Indexed: 08/06/2023] Open
Abstract
BACKGROUND RNA binding proteins (RBPs)-regulated gene expression play a vital role in various pathological processes, including the progression of cancer. However, the role of RBP in hepatocellular carcinoma (HCC) remains much unknown. In this study, we aimed to explore the contribution of RBP CCDC137 in HCC development. METHODS We analyzed the altered expression level and clinical significance of CCDC137 in database and HCC specimens. In vitro cell assays and in vivo spontaneous mouse models were used to assess the function of CCDC137. Finally, the molecular mechanisms of how CCDC137 regulates gene expression and promotes HCC was explored. RESULTS CCDC137 is aberrantly upregulated in HCC and correlates with poor clinical outcomes in HCC patients. CCDC137 markedly promoted HCC proliferation and progression in vitro and in vivo. Mechanistically, CCDC137 binds with FOXM1, JTV1, LASP1 and FLOT2 mRNAs, which was revealed by APOBEC1-mediated profiling, to increase their cytoplasmic localization and thus enhance their protein expressions. Upregulation of FOXM1, JTV1, LASP1 and FLOT2 subsequently synergistically activate AKT signaling and promote HCC. Interestingly, we found that CCDC137 binds with the microprocessor protein DGCR8 and DGCR8 has a novel non-canonical function in mRNA subcellular localization, which mediates the cytoplasmic distribution of mRNAs regulated by CCDC137. CONCLUSIONS Our results identify a critical proliferation-related role of CCDC137 and reveal a novel CCDC137/DGCR8/mRNA localization/AKT axis in HCC progression, which provide a potential target for HCC therapy.
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Affiliation(s)
- Shuang Tao
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, P.R. China
- Present address: Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, P.R. China
| | - Shu-Juan Xie
- Institute of Vaccine, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, P.R. China
| | - Li-Ting Diao
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, P.R. China
| | - Guo Lv
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, P.R. China
| | - Ya-Rui Hou
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, P.R. China
| | - Yan-Xia Hu
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, P.R. China
| | - Wan-Yi Xu
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, P.R. China
| | - Bin Du
- Department of Pathology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, P.R. China.
| | - Zhen-Dong Xiao
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, P.R. China.
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4
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Kim D, Orr MJ, Kwong AJ, Deibler KK, Munshi HH, Bridges CS, Chen TJ, Zhang X, Lacorazza HD, Scheidt KA. Rational Design of Highly Potent and Selective Covalent MAP2K7 Inhibitors. ACS Med Chem Lett 2023; 14:606-613. [PMID: 37197477 PMCID: PMC10184151 DOI: 10.1021/acsmedchemlett.3c00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/10/2023] [Indexed: 05/19/2023] Open
Abstract
The mitogen-activated protein kinase signaling cascade is conserved across eukaryotes, where it plays a critical role in the regulation of activities including proliferation, differentiation, and stress responses. This pathway propagates external stimuli through a series of phosphorylation events, which allows external signals to influence metabolic and transcriptional activities. Within the cascade, MEK, or MAP2K, enzymes occupy a molecular crossroads immediately upstream to significant signal divergence and cross-talk. One such kinase, MAP2K7, also known as MEK7 and MKK7, is a protein of great interest in the molecular pathophysiology underlying pediatric T cell acute lymphoblastic leukemia (T-ALL). Herein, we describe the rational design, synthesis, evaluation, and optimization of a novel class of irreversible MAP2K7 inhibitors. With a streamlined one-pot synthesis, favorable in vitro potency and selectivity, and promising cellular activity, this novel class of compounds wields promise as a powerful tool in the study of pediatric T-ALL.
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Affiliation(s)
- Dalton
R. Kim
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Meghan J. Orr
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Ada J. Kwong
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Kristine K. Deibler
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Hasan H. Munshi
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Cory Seth Bridges
- Department
of Pathology & Immunology, Baylor College
of Medicine, Houston, Texas 77030, United States
| | - Taylor Jie Chen
- Department
of Pathology & Immunology, Baylor College
of Medicine, Houston, Texas 77030, United States
| | - Xiaoyu Zhang
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry
of Life Processes Institute, Northwestern
University, Evanston, Illinois 60208, United
States
| | - H. Daniel Lacorazza
- Department
of Pathology & Immunology, Baylor College
of Medicine, Houston, Texas 77030, United States
| | - Karl A. Scheidt
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry
of Life Processes Institute, Northwestern
University, Evanston, Illinois 60208, United
States
- Department
of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
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5
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HER2-driven breast cancer suppression by the JNK signaling pathway. Proc Natl Acad Sci U S A 2023; 120:e2218373120. [PMID: 36656864 PMCID: PMC9942916 DOI: 10.1073/pnas.2218373120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The HER2+ subtype of human breast cancer is associated with the malignant transformation of luminal ductal cells of the mammary epithelium. The sequence analysis of tumor DNA identifies loss of function mutations and deletions of the MAP2K4 and MAP2K7 genes that encode direct activators of the JUN NH2-terminal kinase (JNK). We report that in vitro studies of human mammary epithelial cells with CRISPR-induced mutations in the MAPK and MAP2K components of the JNK pathway caused no change in growth in 2D culture, but these mutations promoted epithelial cell proliferation in 3D culture. Analysis of gene expression signatures in 3D culture demonstrated similar changes caused by HER2 activation and JNK pathway loss. The mechanism of signal transduction cross-talk may be mediated, in part, by JNK-suppressed expression of integrin α6β4 that binds HER2 and amplifies HER2 signaling. These data suggest that HER2 activation and JNK pathway loss may synergize to promote breast cancer. To test this hypothesis, we performed in vivo studies using a mouse model of HER2+ breast cancer with Cre/loxP-mediated ablation of genes encoding JNK (Mapk8 and Mapk9) and the MAP2K (Map2k4 and Map2k7) that activate JNK in mammary epithelial cells. Kaplan-Meier analysis of tumor development demonstrated that JNK pathway deficiency promotes HER2+-driven breast cancer. Collectively, these data identify JNK pathway genes as potential suppressors for HER2+ breast cancer.
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6
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Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs that regulate gene expression after transcription. miRNAs are present in transcriptionally quiescent full-grown oocytes and preimplantation embryos that display a low level of transcription prior to embryonic genome activation. The role of miRNAs, if any, in preimplantation development is not known. The temporal pattern of expression of miRNAs during bovine preimplantation development was determined by small RNA-sequencing using eggs and preimplantation embryos (1-cell, 2-cell, 4-cell, 8-cell, 16-cell, morula, and blastocyst). Embryos cultured in the presence of α-amanitin, which permitted the distinguishing of maternal miRNAs from embryonic miRNAs, indicated that embryonic miRNA expression was first detected at the two-cell stage but dramatically increased during the morula and blastocyst stages. Targeting DGCR8 by a small-interfering RNA/morpholino approach revealed a role for miRNAs in the morula-to-blastocyst transition. Knockdown of DGCR8 not only inhibited expression of embryonically expressed miRNAs but also inhibited the morula-to-blastocyst transition. In addition, RNA-sequencing identified an increased relative abundance of messenger RNAs potentially targeted by embryonic miRNAs in DGCR8-knockdown embryos when compared with controls. Results from these experiments implicate an essential role for miRNAs in bovine preimplantation embryo development.
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7
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Sjodin BMF, Russello MA. Comparative genomics reveals putative evidence for high-elevation adaptation in the American pika ( Ochotona princeps). G3 GENES|GENOMES|GENETICS 2022; 12:6695220. [PMID: 36087005 PMCID: PMC9635661 DOI: 10.1093/g3journal/jkac241] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/07/2022] [Indexed: 11/30/2022]
Abstract
High-elevation environments have lower atmospheric oxygen content, reduced temperatures, and higher levels of UV radiation than found at lower elevations. As such, species living at high elevations must overcome these challenges to survive, grow, and reproduce. American pikas (Ochotona princeps) are alpine lagomorphs that are habitat specialists typically found at elevations >2,000 m. Previous research has shown putative evidence for high-elevation adaptation; however, investigations to date have been limited to a fraction of the genome. Here, we took a comparative genomics approach to identify putative regions under selection using a chromosomal reference genome assembly for the American pika relative to 8 other mammalian species targeted based on phylogenetic relatedness and (dis)similarity in ecology. We first identified orthologous gene groups across species and then extracted groups containing only American pika genes as well as unclustered pika genes to inform functional enrichment analyses; among these, we found 141 enriched terms with many related to hypoxia, metabolism, mitochondrial function/development, and DNA repair. We identified 15 significantly expanded gene families within the American pika across all orthologous gene groups that displayed functionally enriched terms associated with hypoxia adaptation. We further detected 196 positively selected genes, 41 of which have been associated with putative adaptation to hypoxia, cold tolerance, and response to UV following a literature review. In particular, OXNAD1, NRDC, and those genes critical in DNA repair represent important targets for future research to examine their functional implications in the American pika, especially as they may relate to adaptation to rapidly changing environments.
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Affiliation(s)
- Bryson M F Sjodin
- Department of Biology, University of British Columbia, Okanagan Campus , Kelowna, V1V 1V7 BC, Canada
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus , Kelowna, V1V 1V7 BC, Canada
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8
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Haluck-Kangas A, Patel M, Paudel B, Vaidyanathan A, Murmann AE, Peter ME. DISE/6mer seed toxicity-a powerful anti-cancer mechanism with implications for other diseases. J Exp Clin Cancer Res 2021; 40:389. [PMID: 34893072 PMCID: PMC8662895 DOI: 10.1186/s13046-021-02177-1] [Citation(s) in RCA: 9] [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] [Received: 09/22/2021] [Accepted: 11/05/2021] [Indexed: 01/03/2023] Open
Abstract
micro(mi)RNAs are short noncoding RNAs that through their seed sequence (pos. 2-7/8 of the guide strand) regulate cell function by targeting complementary sequences (seed matches) located mostly in the 3' untranslated region (3' UTR) of mRNAs. Any short RNA that enters the RNA induced silencing complex (RISC) can kill cells through miRNA-like RNA interference when its 6mer seed sequence (pos. 2-7 of the guide strand) has a G-rich nucleotide composition. G-rich seeds mediate 6mer Seed Toxicity by targeting C-rich seed matches in the 3' UTR of genes critical for cell survival. The resulting Death Induced by Survival gene Elimination (DISE) predominantly affects cancer cells but may contribute to cell death in other disease contexts. This review summarizes recent findings on the role of DISE/6mer Seed Tox in cancer; its therapeutic potential; its contribution to therapy resistance; its selectivity, and why normal cells are protected. In addition, we explore the connection between 6mer Seed Toxicity and aging in relation to cancer and certain neurodegenerative diseases.
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Affiliation(s)
- Ashley Haluck-Kangas
- Division Hematology/Oncology and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Lurie 6-123, Chicago, IL 60611 USA
| | - Monal Patel
- Division Hematology/Oncology and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Lurie 6-123, Chicago, IL 60611 USA
| | - Bidur Paudel
- Division Hematology/Oncology and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Lurie 6-123, Chicago, IL 60611 USA
| | - Aparajitha Vaidyanathan
- Division Hematology/Oncology and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Lurie 6-123, Chicago, IL 60611 USA
| | - Andrea E. Murmann
- Division Hematology/Oncology and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Lurie 6-123, Chicago, IL 60611 USA
| | - Marcus E. Peter
- Division Hematology/Oncology and Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 East Superior Street, Lurie 6-123, Chicago, IL 60611 USA
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9
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Non-canonical function of DGCR8 in DNA double-strand break repair signaling and tumor radioresistance. Nat Commun 2021; 12:4033. [PMID: 34188037 PMCID: PMC8242032 DOI: 10.1038/s41467-021-24298-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 06/11/2021] [Indexed: 12/21/2022] Open
Abstract
In response to DNA double-strand breaks (DSBs), repair proteins are recruited to the damaged sites. Ubiquitin signaling plays a critical role in coordinating protein recruitment during the DNA damage response. Here, we find that the microRNA biogenesis factor DGCR8 promotes tumor resistance to X-ray radiation independently of its Drosha-binding ability. Upon radiation, the kinase ATM and the deubiquitinase USP51 mediate the activation and stabilization of DGCR8 through phosphorylation and deubiquitination. Specifically, radiation-induced ATM-dependent phosphorylation of DGCR8 at serine 677 facilitates USP51 to bind, deubiquitinate, and stabilize DGCR8, which leads to the recruitment of DGCR8 and DGCR8’s binding partner RNF168 to MDC1 and RNF8 at DSBs. This, in turn, promotes ubiquitination of histone H2A, repair of DSBs, and radioresistance. Altogether, these findings reveal the non-canonical function of DGCR8 in DSB repair and suggest that radiation treatment may result in therapy-induced tumor radioresistance through ATM- and USP51-mediated activation and upregulation of DGCR8. The molecular mechanisms underlying cancer cell radioresistance need to be elucidated. In this study, the authors show that the microRNA biogenesis factor DGCR8 is stabilized by USP51 and ATM upon irradiation and by consequence it promotes the repair of DNA double-strand breaks and radioresistance by recruiting RNF168 to sites of damage.
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10
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Spatiotemporal 22q11.21 Protein Network Implicates DGCR8-Dependent MicroRNA Biogenesis as a Risk for Late-Fetal Cortical Development in Psychiatric Diseases. Life (Basel) 2021; 11:life11060514. [PMID: 34073122 PMCID: PMC8227527 DOI: 10.3390/life11060514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 12/28/2022] Open
Abstract
The chromosome 22q11.21 copy number variant (CNV) is a vital risk factor that can be a genetic predisposition to neurodevelopmental disorders (NDD). As the 22q11.21 CNV affects multiple genes, causal disease genes and mechanisms affected are still poorly understood. Thus, we aimed to identify the most impactful 22q11.21 CNV genes and the potential impacted human brain regions, developmental stages and signaling pathways. We constructed the spatiotemporal dynamic networks of 22q11.21 CNV genes using the brain developmental transcriptome and physical protein–protein interactions. The affected brain regions, developmental stages, driver genes and pathways were subsequently investigated via integrated bioinformatics analysis. As a result, we first identified that 22q11.21 CNV genes affect the cortical area mainly during late fetal periods. Interestingly, we observed that connections between a driver gene, DGCR8, and its interacting partners, MECP2 and CUL3, also network hubs, only existed in the network of the late fetal period within the cortical region, suggesting their functional specificity during brain development. We also confirmed the physical interaction result between DGCR8 and CUL3 by liquid chromatography-tandem mass spectrometry. In conclusion, our results could suggest that the disruption of DGCR8-dependent microRNA biogenesis plays a vital role in NDD for late fetal cortical development.
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11
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Wang L, Li X, Zhao L, Jiang L, Song X, Qi A, Chen T, Ju M, Hu B, Wei M, He M, Zhao L. Identification of DNA-Repair-Related Five-Gene Signature to Predict Prognosis in Patients with Esophageal Cancer. Pathol Oncol Res 2021; 27:596899. [PMID: 34257547 PMCID: PMC8262199 DOI: 10.3389/pore.2021.596899] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 02/10/2021] [Indexed: 12/13/2022]
Abstract
Esophageal cancer (ESCA) is a leading cause of cancer-related mortality, with poor prognosis worldwide. DNA damage repair is one of the hallmarks of cancer. Loss of genomic integrity owing to inactivation of DNA repair genes can increase the risk of cancer progression and lead to poor prognosis. We aimed to identify a novel gene signature related to DNA repair to predict the prognosis of ESCA patients. Based on gene expression profiles of ESCA patients from The Cancer Genome Atlas and gene set enrichment analysis, 102 genes related to DNA repair were identified as candidates. After stepwise Cox regression analysis, we established a five-gene prognostic model comprising DGCR8, POM121, TAF9, UPF3B, and BCAP31. Kaplan-Meier survival analysis confirmed a strong correlation between the prognostic model and survival. Moreover, we verified the clinical value of the prognostic signature under the influence of different clinical parameters. We found that small-molecule drugs (trametinib, selumetinib, and refametinib) could help to improve patient survival. In summary, our study provides a novel and promising prognostic signature based on DNA-repair-related genes to predict survival of patients with ESCA. Systematic data mining provides a theoretical basis for further exploring the molecular pathogenesis of ESCA and identifying therapeutic targets.
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Affiliation(s)
- Lin Wang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Xueping Li
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Lan Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Longyang Jiang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Xinyue Song
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Aoshuang Qi
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Ting Chen
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Mingyi Ju
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Baohui Hu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Miao He
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
| | - Lin Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, China
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12
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Pabit SA, Chen YL, Usher ET, Cook EC, Pollack L, Showalter SA. Elucidating the Role of Microprocessor Protein DGCR8 in Bending RNA Structures. Biophys J 2020; 119:2524-2536. [PMID: 33189689 DOI: 10.1016/j.bpj.2020.10.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/23/2020] [Accepted: 10/30/2020] [Indexed: 10/23/2022] Open
Abstract
Although conformational dynamics of RNA molecules are potentially important in microRNA (miRNA) processing, the role of the protein binding partners in facilitating the requisite structural changes is not well understood. In previous work, we and others have demonstrated that nonduplex structural elements and the conformational flexibility they support are necessary for efficient RNA binding and cleavage by the proteins associated with the two major stages of miRNA processing. However, recent studies showed that the protein DGCR8 binds primary miRNA and duplex RNA with similar affinities. Here, we study RNA binding by a small recombinant construct of the DGCR8 protein and the RNA conformation changes that result. This construct, the DGCR8 core, contains two double-stranded RNA-binding domains (dsRBDs) and a C-terminal tail. To assess conformational changes resulting from binding, we applied small-angle x-ray scattering with contrast variation to detect conformational changes of primary-miR-16-1 in complex with the DGCR8 core. This method reports only on the RNA conformation within the complex and suggests that the protein bends the RNA upon binding. Supporting work using smFRET to study the conformation of RNA duplexes bound to the core also shows bending. Together, these studies elucidate the role of DGCR8 in interacting with RNA during the early stages of miRNA processing.
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Affiliation(s)
- Suzette A Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York
| | - Yen-Lin Chen
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York
| | - Emery T Usher
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania
| | - Erik C Cook
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York.
| | - Scott A Showalter
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania; Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania.
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13
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APOE4 exacerbates synapse loss and neurodegeneration in Alzheimer's disease patient iPSC-derived cerebral organoids. Nat Commun 2020; 11:5540. [PMID: 33139712 PMCID: PMC7608683 DOI: 10.1038/s41467-020-19264-0] [Citation(s) in RCA: 173] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 10/02/2020] [Indexed: 12/25/2022] Open
Abstract
APOE4 is the strongest genetic risk factor associated with late-onset Alzheimer’s disease (AD). To address the underlying mechanism, we develop cerebral organoid models using induced pluripotent stem cells (iPSCs) with APOE ε3/ε3 or ε4/ε4 genotype from individuals with either normal cognition or AD dementia. Cerebral organoids from AD patients carrying APOE ε4/ε4 show greater apoptosis and decreased synaptic integrity. While AD patient-derived cerebral organoids have increased levels of Aβ and phosphorylated tau compared to healthy subject-derived cerebral organoids, APOE4 exacerbates tau pathology in both healthy subject-derived and AD patient-derived organoids. Transcriptomics analysis by RNA-sequencing reveals that cerebral organoids from AD patients are associated with an enhancement of stress granules and disrupted RNA metabolism. Importantly, isogenic conversion of APOE4 to APOE3 attenuates the APOE4-related phenotypes in cerebral organoids from AD patients. Together, our study using human iPSC-organoids recapitulates APOE4-related phenotypes and suggests APOE4-related degenerative pathways contributing to AD pathogenesis. APOE4 is a strong genetic risk factor for late-onset Alzheimer’s disease. Here, the authors show that APOE4 is associated with AD features in hiPSCs-derived cerebral organoids. Isogenic conversion of APOE4 to APOE3 attenuates the AD-associated phenotype.
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14
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Vågbø CB, Slupphaug G. RNA in DNA repair. DNA Repair (Amst) 2020; 95:102927. [DOI: 10.1016/j.dnarep.2020.102927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/07/2020] [Accepted: 07/08/2020] [Indexed: 12/22/2022]
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15
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Lambo S, von Hoff K, Korshunov A, Pfister SM, Kool M. ETMR: a tumor entity in its infancy. Acta Neuropathol 2020; 140:249-266. [PMID: 32601913 PMCID: PMC7423804 DOI: 10.1007/s00401-020-02182-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/04/2020] [Accepted: 06/18/2020] [Indexed: 12/18/2022]
Abstract
Embryonal tumor with Multilayered Rosettes (ETMR) is a relatively rare but typically deadly type of brain tumor that occurs mostly in infants. Since the discovery of the characteristic chromosome 19 miRNA cluster (C19MC) amplification a decade ago, the methods for diagnosing this entity have improved and many new insights in the molecular landscape of ETMRs have been acquired. All ETMRs, despite their highly heterogeneous histology, are characterized by specific high expression of the RNA-binding protein LIN28A, which is, therefore, often used as a diagnostic marker for these tumors. ETMRs have few recurrent genetic aberrations, mainly affecting the miRNA pathway and including amplification of C19MC (embryonal tumor with multilayered rosettes, C19MC-altered) and mutually exclusive biallelic DICER1 mutations of which the first hit is typically inherited through the germline (embryonal tumor with multilayered rosettes, DICER1-altered). Identification of downstream pathways affected by the deregulated miRNA machinery has led to several proposed potential therapeutical vulnerabilities including targeting the WNT, SHH, or mTOR pathways, MYCN or chromosomal instability. However, despite those findings, treatment outcomes have only marginally improved, since the initial description of this tumor entity. Many patients do not survive longer than a year after diagnosis and the 5-year overall survival rate is still lower than 30%. Thus, there is an urgent need to translate the new insights in ETMR biology into more effective treatments. Here, we present an overview of clinical and molecular characteristics of ETMRs and the current progress on potential targeted therapies.
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Affiliation(s)
- Sander Lambo
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Katja von Hoff
- Department of Pediatric Oncology/Hematology, Charité University Medicine, Berlin, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
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16
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Lee JW, Ratnakumar K, Hung KF, Rokunohe D, Kawasumi M. Deciphering UV-induced DNA Damage Responses to Prevent and Treat Skin Cancer. Photochem Photobiol 2020; 96:478-499. [PMID: 32119110 DOI: 10.1111/php.13245] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/11/2020] [Indexed: 12/11/2022]
Abstract
Ultraviolet (UV) radiation is among the most prevalent environmental factors that influence human health and disease. Even 1 h of UV irradiation extensively damages the genome. To cope with resulting deleterious DNA lesions, cells activate a multitude of DNA damage response pathways, including DNA repair. Strikingly, UV-induced DNA damage formation and repair are affected by chromatin state. When cells enter S phase with these lesions, a distinct mutation signature is created via error-prone translesion synthesis. Chronic UV exposure leads to high mutation burden in skin and consequently the development of skin cancer, the most common cancer in the United States. Intriguingly, UV-induced oxidative stress has opposing effects on carcinogenesis. Elucidating the molecular mechanisms of UV-induced DNA damage responses will be useful for preventing and treating skin cancer with greater precision. Excitingly, recent studies have uncovered substantial depth of novel findings regarding the molecular and cellular consequences of UV irradiation. In this review, we will discuss updated mechanisms of UV-induced DNA damage responses including the ATR pathway, which maintains genome integrity following UV irradiation. We will also present current strategies for preventing and treating nonmelanoma skin cancer, including ATR pathway inhibition for prevention and photodynamic therapy for treatment.
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Affiliation(s)
- Jihoon W Lee
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA
| | - Kajan Ratnakumar
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA
| | - Kai-Feng Hung
- Division of Translational Research, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Dentistry, National Yang-Ming University, Taipei, Taiwan
| | - Daiki Rokunohe
- Department of Dermatology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Masaoki Kawasumi
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA
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17
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Collin GB, Gogna N, Chang B, Damkham N, Pinkney J, Hyde LF, Stone L, Naggert JK, Nishina PM, Krebs MP. Mouse Models of Inherited Retinal Degeneration with Photoreceptor Cell Loss. Cells 2020; 9:cells9040931. [PMID: 32290105 PMCID: PMC7227028 DOI: 10.3390/cells9040931] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 12/12/2022] Open
Abstract
Inherited retinal degeneration (RD) leads to the impairment or loss of vision in millions of individuals worldwide, most frequently due to the loss of photoreceptor (PR) cells. Animal models, particularly the laboratory mouse, have been used to understand the pathogenic mechanisms that underlie PR cell loss and to explore therapies that may prevent, delay, or reverse RD. Here, we reviewed entries in the Mouse Genome Informatics and PubMed databases to compile a comprehensive list of monogenic mouse models in which PR cell loss is demonstrated. The progression of PR cell loss with postnatal age was documented in mutant alleles of genes grouped by biological function. As anticipated, a wide range in the onset and rate of cell loss was observed among the reported models. The analysis underscored relationships between RD genes and ciliary function, transcription-coupled DNA damage repair, and cellular chloride homeostasis. Comparing the mouse gene list to human RD genes identified in the RetNet database revealed that mouse models are available for 40% of the known human diseases, suggesting opportunities for future research. This work may provide insight into the molecular players and pathways through which PR degenerative disease occurs and may be useful for planning translational studies.
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Affiliation(s)
- Gayle B. Collin
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
| | - Navdeep Gogna
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
| | - Bo Chang
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
| | - Nattaya Damkham
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Jai Pinkney
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
| | - Lillian F. Hyde
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
| | - Lisa Stone
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
| | - Jürgen K. Naggert
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
| | - Patsy M. Nishina
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
- Correspondence: (P.M.N.); (M.P.K.); Tel.: +1-207-2886-383 (P.M.N.); +1-207-2886-000 (M.P.K.)
| | - Mark P. Krebs
- The Jackson Laboratory, Bar Harbor, Maine, ME 04609, USA; (G.B.C.); (N.G.); (B.C.); (N.D.); (J.P.); (L.F.H.); (L.S.); (J.K.N.)
- Correspondence: (P.M.N.); (M.P.K.); Tel.: +1-207-2886-383 (P.M.N.); +1-207-2886-000 (M.P.K.)
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18
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Gutbrod MJ, Martienssen RA. Conserved chromosomal functions of RNA interference. Nat Rev Genet 2020; 21:311-331. [PMID: 32051563 DOI: 10.1038/s41576-019-0203-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2019] [Indexed: 12/21/2022]
Abstract
RNA interference (RNAi), a cellular process through which small RNAs target and regulate complementary RNA transcripts, has well-characterized roles in post-transcriptional gene regulation and transposon repression. Recent studies have revealed additional conserved roles for RNAi proteins, such as Argonaute and Dicer, in chromosome function. By guiding chromatin modification, RNAi components promote chromosome segregation during both mitosis and meiosis and regulate chromosomal and genomic dosage response. Small RNAs and the RNAi machinery also participate in the resolution of DNA damage. Interestingly, many of these lesser-studied functions seem to be more strongly conserved across eukaryotes than are well-characterized functions such as the processing of microRNAs. These findings have implications for the evolution of RNAi since the last eukaryotic common ancestor, and they provide a more complete view of the functions of RNAi.
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Affiliation(s)
- Michael J Gutbrod
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Robert A Martienssen
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. .,Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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19
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Burger K, Ketley RF, Gullerova M. Beyond the Trinity of ATM, ATR, and DNA-PK: Multiple Kinases Shape the DNA Damage Response in Concert With RNA Metabolism. Front Mol Biosci 2019; 6:61. [PMID: 31428617 PMCID: PMC6688092 DOI: 10.3389/fmolb.2019.00061] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/11/2019] [Indexed: 12/22/2022] Open
Abstract
Our genome is constantly exposed to endogenous and exogenous sources of DNA damage resulting in various alterations of the genetic code. DNA double-strand breaks (DSBs) are considered one of the most cytotoxic lesions. Several types of repair pathways act to repair DNA damage and maintain genome stability. In the canonical DNA damage response (DDR) DSBs are recognized by the sensing kinases Ataxia-telangiectasia mutated (ATM), Ataxia-telangiectasia and Rad3-related (ATR), and DNA-dependent protein kinase (DNA-PK), which initiate a cascade of kinase-dependent amplification steps known as DSB signaling. Recent evidence suggests that efficient recognition and repair of DSBs relies on the transcription and processing of non-coding (nc)RNA molecules by RNA polymerase II (RNAPII) and the RNA interference (RNAi) factors Drosha and Dicer. Multiple kinases influence the phosphorylation status of both the RNAPII carboxy-terminal domain (CTD) and Dicer in order to regulate RNA-dependent DSBs repair. The importance of kinase signaling and RNA processing in the DDR is highlighted by the regulation of p53-binding protein (53BP1), a key regulator of DSB repair pathway choice between homologous recombination (HR) and non-homologous end joining (NHEJ). Additionally, emerging evidence suggests that RNA metabolic enzymes also play a role in the repair of other types of DNA damage, including the DDR to ultraviolet radiation (UVR). RNAi factors are also substrates for mitogen-activated protein kinase (MAPK) signaling and mediate the turnover of ncRNA during nucleotide excision repair (NER) in response to UVR. Here, we review kinase-dependent phosphorylation events on RNAPII, Drosha and Dicer, and 53BP1 that modulate the key steps of the DDR to DSBs and UVR, suggesting an intimate link between the DDR and RNA metabolism.
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Affiliation(s)
| | | | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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20
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Deng L, Ren R, Liu Z, Song M, Li J, Wu Z, Ren X, Fu L, Li W, Zhang W, Guillen P, Izpisua Belmonte JC, Chan P, Qu J, Liu GH. Stabilizing heterochromatin by DGCR8 alleviates senescence and osteoarthritis. Nat Commun 2019; 10:3329. [PMID: 31350386 PMCID: PMC6659673 DOI: 10.1038/s41467-019-10831-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/03/2019] [Indexed: 01/01/2023] Open
Abstract
DiGeorge syndrome critical region 8 (DGCR8) is a critical component of the canonical microprocessor complex for microRNA biogenesis. However, the non-canonical functions of DGCR8 have not been studied. Here, we demonstrate that DGCR8 plays an important role in maintaining heterochromatin organization and attenuating aging. An N-terminal-truncated version of DGCR8 (DR8dex2) accelerated senescence in human mesenchymal stem cells (hMSCs) independent of its microRNA-processing activity. Further studies revealed that DGCR8 maintained heterochromatin organization by interacting with the nuclear envelope protein Lamin B1, and heterochromatin-associated proteins, KAP1 and HP1γ. Overexpression of any of these proteins, including DGCR8, reversed premature senescent phenotypes in DR8dex2 hMSCs. Finally, DGCR8 was downregulated in pathologically and naturally aged hMSCs, whereas DGCR8 overexpression alleviated hMSC aging and mouse osteoarthritis. Taken together, these analyses uncovered a novel, microRNA processing-independent role in maintaining heterochromatin organization and attenuating senescence by DGCR8, thus representing a new therapeutic target for alleviating human aging-related disorders.
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Affiliation(s)
- Liping Deng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Ruotong Ren
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Zunpeng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Moshi Song
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
| | - Jingyi Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, 100053, Beijing, China
| | - Zeming Wu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiaoqing Ren
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Lina Fu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Wei Li
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, 100053, Beijing, China
| | - Weiqi Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, 100053, Beijing, China
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Pedro Guillen
- Clinica Cemtro. Av. del Ventisquero de la Condesa, 42, 28035, Madrid, Spain
| | | | - Piu Chan
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, 100053, Beijing, China
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Guang-Hui Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China.
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, 100053, Beijing, China.
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, 510632, Guangzhou, China.
- Beijing Institute for Brain Disorders, Capital Medical University, 100069, Beijing, China.
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21
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Liu D, Yao K, Li J, Huang Y, Brennan CS, Chen S, Wu H, Zeng X, Brennan M, Li L. The effect of ultraviolet modification of
Acetobacter xylinum
(CGMCC No. 7431) and the use of coconut milk on the yield and quality of bacterial cellulose. Int J Food Sci Technol 2019. [DOI: 10.1111/ijfs.14225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Dong‐mei Liu
- School of Food Science and Engineering South China University of Technology 381 Wushan Road Guangzhou Guangdong 510640 China
| | - Kun Yao
- School of Food Science and Engineering South China University of Technology 381 Wushan Road Guangzhou Guangdong 510640 China
| | - Jia‐hui Li
- School of Food Science and Engineering South China University of Technology 381 Wushan Road Guangzhou Guangdong 510640 China
| | - Yan‐yan Huang
- School of Food Science and Engineering South China University of Technology 381 Wushan Road Guangzhou Guangdong 510640 China
| | - Charles S. Brennan
- School of Food Science and Engineering South China University of Technology 381 Wushan Road Guangzhou Guangdong 510640 China
- Department of Wine, Food and Molecular Biosciences, Centre for Food Research and Innovation Lincoln University Lincoln 85084 New Zealand
| | - Si‐min Chen
- School of Food Science and Engineering South China University of Technology 381 Wushan Road Guangzhou Guangdong 510640 China
| | - Hui Wu
- School of Food Science and Engineering South China University of Technology 381 Wushan Road Guangzhou Guangdong 510640 China
| | - Xin‐An Zeng
- School of Food Science and Engineering South China University of Technology 381 Wushan Road Guangzhou Guangdong 510640 China
| | - Margaret Brennan
- Department of Wine, Food and Molecular Biosciences, Centre for Food Research and Innovation Lincoln University Lincoln 85084 New Zealand
| | - Li Li
- School of Food Science and Engineering South China University of Technology 381 Wushan Road Guangzhou Guangdong 510640 China
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22
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Bonath F, Domingo-Prim J, Tarbier M, Friedländer MR, Visa N. Next-generation sequencing reveals two populations of damage-induced small RNAs at endogenous DNA double-strand breaks. Nucleic Acids Res 2019; 46:11869-11882. [PMID: 30418607 PMCID: PMC6294500 DOI: 10.1093/nar/gky1107] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 10/22/2018] [Indexed: 12/20/2022] Open
Abstract
Recent studies suggest that transcription takes place at DNA double-strand breaks (DSBs), that transcripts at DSBs are processed by Drosha and Dicer into damage-induced small RNAs (diRNAs), and that diRNAs are required for DNA repair. However, diRNAs have been mostly detected in reporter constructs or repetitive sequences, and their existence at endogenous loci has been questioned by recent reports. Using the homing endonuclease I-PpoI, we have investigated diRNA production in genetically unperturbed human and mouse cells. I-PpoI is an ideal tool to clarify the requirements for diRNA production because it induces DSBs in different types of loci: the repetitive 28S locus, unique genes and intergenic loci. We show by extensive sequencing that the rDNA locus produces substantial levels of diRNAs, whereas unique genic and intergenic loci do not. Further characterization of diRNAs emerging from the 28S locus reveals the existence of two diRNA subtypes. Surprisingly, Drosha and its partner DGCR8 are dispensable for diRNA production and only one diRNAs subtype depends on Dicer processing. Furthermore, we provide evidence that diRNAs are incorporated into Argonaute. Our findings provide direct evidence for diRNA production at endogenous loci in mammalian cells and give insights into RNA processing at DSBs.
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Affiliation(s)
- Franziska Bonath
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Judit Domingo-Prim
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Marcel Tarbier
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
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23
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Guo WT, Wang Y. Dgcr8 knockout approaches to understand microRNA functions in vitro and in vivo. Cell Mol Life Sci 2019; 76:1697-1711. [PMID: 30694346 PMCID: PMC11105204 DOI: 10.1007/s00018-019-03020-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 01/11/2019] [Accepted: 01/17/2019] [Indexed: 01/07/2023]
Abstract
Biologic function of the majority of microRNAs (miRNAs) is still unknown. Uncovering the function of miRNAs is hurdled by redundancy among different miRNAs. The deletion of Dgcr8 leads to the deficiency in producing all canonical miRNAs, therefore, overcoming the redundancy issue. Dgcr8 knockout strategy has been instrumental in understanding the function of miRNAs in a variety of cells in vitro and in vivo. In this review, we will first give a brief introduction about miRNAs, miRNA biogenesis pathway and the role of Dgcr8 in miRNA biogenesis. We will then summarize studies performed with Dgcr8 knockout cell models with a focus on embryonic stem cells. After that, we will summarize results from various in vivo Dgcr8 knockout models. Given significant phenotypic differences in various tissues between Dgcr8 and Dicer knockout, we will also briefly review current progresses on understanding miRNA-independent functions of miRNA biogenesis factors. Finally, we will discuss the potential use of a new strategy to stably express miRNAs in Dgcr8 knockout cells. In future, Dgcr8 knockout approaches coupled with innovations in miRNA rescue strategy may provide further insights into miRNA functions in vitro and in vivo.
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Affiliation(s)
- Wen-Ting Guo
- Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, People's Republic of China
| | - Yangming Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, 100871, People's Republic of China.
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24
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Pong SK, Gullerova M. Noncanonical functions of microRNA pathway enzymes - Drosha, DGCR8, Dicer and Ago proteins. FEBS Lett 2018; 592:2973-2986. [PMID: 30025156 DOI: 10.1002/1873-3468.13196] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 07/10/2018] [Accepted: 07/12/2018] [Indexed: 01/15/2023]
Abstract
MicroRNAs (miRNAs) are small regulatory noncoding RNAs that are generated in the canonical RNA interference (RNAi) pathway. Drosha, DiGeorge syndrome critical region 8 (DGCR8) and Dicer are key players in miRNA biogenesis. Argonaute (Ago) proteins bind to miRNAs and are guided by them to find messenger RNA targets and carry out post-transcriptional silencing of protein-coding genes. Recently, emerging evidence suggests that RNAi factors have a range of noncanonical functions that are beyond miRNA biogenesis. These functions pertain to various biological processes, such as development, transcriptional regulation, RNA processing and maintenance of genome integrity. Here, we review recent literature reporting miRNA-independent, noncanonical functions of Drosha, DGCR8, Dicer and Ago proteins and discuss the importance of these functions.
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Affiliation(s)
- Sheng K Pong
- Sir William Dunn School of Pathology, University of Oxford, UK
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25
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Girnius N, Edwards YJ, Garlick DS, Davis RJ. The cJUN NH 2-terminal kinase (JNK) signaling pathway promotes genome stability and prevents tumor initiation. eLife 2018; 7:36389. [PMID: 29856313 PMCID: PMC5984035 DOI: 10.7554/elife.36389] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 05/09/2018] [Indexed: 12/19/2022] Open
Abstract
Breast cancer is the most commonly diagnosed malignancy in women. Analysis of breast cancer genomic DNA indicates frequent loss-of-function mutations in components of the cJUN NH2-terminal kinase (JNK) signaling pathway. Since JNK signaling can promote cell proliferation by activating the AP1 transcription factor, this apparent association of reduced JNK signaling with tumor development was unexpected. We examined the effect of JNK deficiency in the murine breast epithelium. Loss of JNK signaling caused genomic instability and the development of breast cancer. Moreover, JNK deficiency caused widespread early neoplasia and rapid tumor formation in a murine model of breast cancer. This tumor suppressive function was not mediated by a role of JNK in the growth of established tumors, but by a requirement of JNK to prevent tumor initiation. Together, these data identify JNK pathway defects as ‘driver’ mutations that promote genome instability and tumor initiation. As cells in our body grow and divide, their DNA can experience changes or damage. Most of these ‘mutations’ are harmless, or quickly fixed by the body. Yet, sometimes a mutation can trigger a chain of genetic events that drives the cells to multiply uncontrollably, which leads to tumors. Identifying these ‘driver mutations’ is complex, but key to understanding how cancers start and can be fought. Breast cancer is the most common type of cancer diagnosed in women worldwide. Large studies have focused on sequencing the DNA of cancerous breast cells to try to identify the mutations that started the cancer. Results show that, in these cells, a biological mechanism called the JNK signaling pathway is often inactivated because mutations affect the molecules that take part in this process. Like a chain reaction, the proteins of the JNK pathway act on each other until the last one, called JNK, gets switched on. This protein then goes on to participate in a number of cellular processes such as DNA repair. Is it possible that mutations in this pathway actually drive cancer, and if so, how? Girnius et al. addressed these questions by inactivating the JNK pathway in the breast cells of mice. Over the next year and a half, the JNK-deficient animals were more likely to get breast cancer than normal mice. Further experiments showed that, in breast cells, the JNK protein prevented tumors from appearing. However, once the tumors were present, it was less effective at stopping them from growing. The DNA of the breast cancer cells with no JNK protein also contained more genetic changes and mistakes. This suggests that the JNK signaling pathway helps to keep the genetic information ‘healthy’. This may be because, normally, the JNK protein activates processes that fix DNA mutations. Taken together, the results presented by Girnius et al. show that genetic changes which inactivate the JNK pathway can drive the development of breast cancer. Certain anti-cancer drugs kill cancerous cells by damaging their DNA. Breast tumor cells with inactive JNK pathways are less able to repair their genetic information, and so these drugs could potentially work well on them. Future experiments will be needed to test this hypothesis.
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Affiliation(s)
- Nomeda Girnius
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Yvonne Jk Edwards
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - David S Garlick
- Histo-Scientific Research Laboratories, Mount Jackson, United States
| | - Roger J Davis
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States.,Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
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26
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Gregersen LH, Svejstrup JQ. The Cellular Response to Transcription-Blocking DNA Damage. Trends Biochem Sci 2018; 43:327-341. [PMID: 29699641 PMCID: PMC5929563 DOI: 10.1016/j.tibs.2018.02.010] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/16/2018] [Accepted: 02/19/2018] [Indexed: 12/27/2022]
Abstract
In response to transcription-blocking DNA lesions such as those generated by UV irradiation, cells activate a multipronged DNA damage response. This response encompasses repair of the lesions that stall RNA polymerase (RNAP) but also a poorly understood, genome-wide shutdown of transcription, even of genes that are not damaged. Over the past few years, a number of new results have shed light on this intriguing DNA damage response at the structural, biochemical, cell biological, and systems biology level. In this review we summarize the most important findings.
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Affiliation(s)
- Lea H Gregersen
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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27
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Hoffmann N, Weise SC, Marinaro F, Vogel T, De Pietri Tonelli D. DGCR8 Promotes Neural Progenitor Expansion and Represses Neurogenesis in the Mouse Embryonic Neocortex. Front Neurosci 2018; 12:281. [PMID: 29760646 PMCID: PMC5936999 DOI: 10.3389/fnins.2018.00281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 04/10/2018] [Indexed: 11/17/2022] Open
Abstract
DGCR8 and DROSHA are the minimal functional core of the Microprocessor complex essential for biogenesis of canonical microRNAs and for the processing of other RNAs. Conditional deletion of Dgcr8 and Drosha in the murine telencephalon indicated that these proteins exert crucial functions in corticogenesis. The identification of mechanisms of DGCR8- or DROSHA-dependent regulation of gene expression in conditional knockout mice are often complicated by massive apoptosis. Here, to investigate DGCR8 functions on amplification/differentiation of neural progenitors cells (NPCs) in corticogenesis, we overexpress Dgcr8 in the mouse telencephalon, by in utero electroporation (IUEp). We find that DGCR8 promotes the expansion of NPC pools and represses neurogenesis, in absence of apoptosis, thus overcoming the usual limitations of Dgcr8 knockout-based approach. Interestingly, DGCR8 selectively promotes basal progenitor amplification at later developmental stages, entailing intriguing implications for neocortical expansion in evolution. Finally, despite a 3- to 5-fold increase of DGCR8 level in the mouse telencephalon, the composition, target preference and function of the DROSHA-dependent Microprocessor complex remain unaltered. Thus, we propose that DGCR8-dependent modulation of gene expression in corticogenesis is more complex than previously known, and possibly DROSHA-independent.
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Affiliation(s)
- Nadin Hoffmann
- Neurobiology of miRNA Laboratory, Department of Neuroscience and Brain Technologies, Fondazione Istituto Italiano di Tecnologia, Genoa, Italy
| | - Stefan C Weise
- Department of Molecular Embryology, Medical Faculty, Institute for Anatomy and Cell Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Federica Marinaro
- Neurobiology of miRNA Laboratory, Department of Neuroscience and Brain Technologies, Fondazione Istituto Italiano di Tecnologia, Genoa, Italy
| | - Tanja Vogel
- Department of Molecular Embryology, Medical Faculty, Institute for Anatomy and Cell Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Davide De Pietri Tonelli
- Neurobiology of miRNA Laboratory, Department of Neuroscience and Brain Technologies, Fondazione Istituto Italiano di Tecnologia, Genoa, Italy
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28
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Michelini F, Jalihal AP, Francia S, Meers C, Neeb ZT, Rossiello F, Gioia U, Aguado J, Jones-Weinert C, Luke B, Biamonti G, Nowacki M, Storici F, Carninci P, Walter NG, d'Adda di Fagagna F. From "Cellular" RNA to "Smart" RNA: Multiple Roles of RNA in Genome Stability and Beyond. Chem Rev 2018; 118:4365-4403. [PMID: 29600857 DOI: 10.1021/acs.chemrev.7b00487] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Coding for proteins has been considered the main function of RNA since the "central dogma" of biology was proposed. The discovery of noncoding transcripts shed light on additional roles of RNA, ranging from the support of polypeptide synthesis, to the assembly of subnuclear structures, to gene expression modulation. Cellular RNA has therefore been recognized as a central player in often unanticipated biological processes, including genomic stability. This ever-expanding list of functions inspired us to think of RNA as a "smart" phone, which has replaced the older obsolete "cellular" phone. In this review, we summarize the last two decades of advances in research on the interface between RNA biology and genome stability. We start with an account of the emergence of noncoding RNA, and then we discuss the involvement of RNA in DNA damage signaling and repair, telomere maintenance, and genomic rearrangements. We continue with the depiction of single-molecule RNA detection techniques, and we conclude by illustrating the possibilities of RNA modulation in hopes of creating or improving new therapies. The widespread biological functions of RNA have made this molecule a reoccurring theme in basic and translational research, warranting it the transcendence from classically studied "cellular" RNA to "smart" RNA.
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Affiliation(s)
- Flavia Michelini
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy
| | - Ameya P Jalihal
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Sofia Francia
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy.,Istituto di Genetica Molecolare , CNR - Consiglio Nazionale delle Ricerche , Pavia , 27100 , Italy
| | - Chance Meers
- School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Zachary T Neeb
- Institute of Cell Biology , University of Bern , Baltzerstrasse 4 , 3012 Bern , Switzerland
| | | | - Ubaldo Gioia
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy
| | - Julio Aguado
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy
| | | | - Brian Luke
- Institute of Developmental Biology and Neurobiology , Johannes Gutenberg University , 55099 Mainz , Germany.,Institute of Molecular Biology (IMB) , 55128 Mainz , Germany
| | - Giuseppe Biamonti
- Istituto di Genetica Molecolare , CNR - Consiglio Nazionale delle Ricerche , Pavia , 27100 , Italy
| | - Mariusz Nowacki
- Institute of Cell Biology , University of Bern , Baltzerstrasse 4 , 3012 Bern , Switzerland
| | - Francesca Storici
- School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Piero Carninci
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho, Tsurumi-ku , Yokohama City , Kanagawa 230-0045 , Japan
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Fabrizio d'Adda di Fagagna
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy.,Istituto di Genetica Molecolare , CNR - Consiglio Nazionale delle Ricerche , Pavia , 27100 , Italy
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